Chloroplast DNA phylogeography of European ashes, Fraxinus sp. (Oleaceae): roles of hybridization and life history traits

We investigated range-wide phylogeographic variation in three European ash species (Fraxinus sp., Oleaceae). Chloroplast DNA (cpDNA) microsatellites were typed in the thermophilous Fraxinus angustifolia and Fraxinus ornus and the observed haplotypes and the geographic distribution of diversity were compared to cpDNA data previously obtained in the more cold-tolerant Fraxinus excelsior. We found wide-ranging haplotype sharing between the phylogenetically close F. angustifolia and F. excelsior, suggesting hybridization (i) in common glacial refuges in the Iberian Peninsula, northern Italy, the eastern and/or Dinaric Alps and the Balkan Peninsula, and/or (ii) during postglacial recolonization. The data allowed us to propose additional glacial refuges for F. angustifolia in southern Italy and in Turkey, and populations from the latter region were particularly polymorphic. There was evidence for refuge areas in Italy, the Balkan Peninsula and Turkey for F. ornus, which did not share any single chloroplast haplotype with the other species. In both F. angustifolia and F. ornus, cpDNA diversity (h(S) = 0.027 and h(S) = 0.009, respectively) was lower and fixation levels (G(ST) = 0.964 and G(ST) = 0.983, respectively) higher than in sympatric F. excelsior (h(S) = 0.096, G(ST) = 0.870). These diversity patterns could be due to temperature tolerance or the demographic history.     

The conservation of the chamois Rupicapra spp.

• 1 Despite it being the most abundant mountain dwelling ungulate of Europe and the Near East, the taxonomy, systematics and biology of the chamois are still imperfectly known. Although neither species of chamois is at risk, several subspecies are threatened (Rupicapra rupicapra cartusiana, Rupicapra rupicapra tatrica and Rupicapra rupicapra balcanica; Rupicapra pyrenaica ornata. Rupicapra rupicapra asiatica is data‐deficient but probably threatened).
• 2 A life history with apparently contradictory relationships between survival, sexual dimorphism and mating system suggests a unique survival strategy not yet fully understood. Over the last century, morphologic, biometric, behavioural and genetic features have been studied to shed light on the phylogeography and monophyly or polyphyly of the chamois as well as on the number of existing species and subspecies of the genus Rupicapra.
• 3 The dispersal hypothesis, according to which R. rupicapra migrated westward from eastern Europe in the Quaternary, confining R. pyrenaica to the southernmost regions of Europe, has been recently called into question by some molecular analyses that yielded contradictory results.
• 4 In spite of subtleties relevant to each method of analysis, an overall evaluation of differences between the R. rupicapra and the R. pyrenaica groups strongly supports the functional separation of the taxa into two species.
• 5 Further studies on the ecology of chamois, as well as on the epidemiology of severe diseases, e.g. sarcoptic mange, are needed to improve the management of viable populations.
• 6 Before translocations and reintroductions are carried out, the risk of hybridization leading to genetic extinction should be evaluated.

     

Geographical patterns of genetic structure in marine species with contrasting life histories

Aim  Phylogeographical breaks may reflect historical or present-day impediments to gene flow, and the congruence of these breaks across multiple species lends insight into evolutionary history and connectivity among populations. In marine systems, examining the concordance of phylogeographical breaks is challenging due to the varied sampling scales in population genetics studies and the diverse life histories of marine organisms. A quantitative approach that considers the effects of sampling scale and species life history is needed.
Location  The south-east and south-west coasts of the United States.
Methods  We quantitatively analysed previously published datasets of marine fauna to look for concordance among phylogeographical breaks. We used a bootstrap approach to determine the regions where phylogeographical breaks are more common than expected by chance among species with planktonic dispersal as well as those with restricted dispersal.
Results  On the south-west coast, breaks were clustered near Point Conception among planktonic dispersers and near Los Angeles among restricted dispersers. On the south-east coast, breaks were most common near the southern tip of Florida for planktonic dispersers and near Cape Canaveral for restricted dispersers.
Main conclusions  Dispersal ability is an important determinant of phylogeographical patterns in marine species. Breaks among planktonic dispersers on both coasts are congruent with present-day flow-mediated barriers to dispersal, suggesting that phylogeographical structure in species with planktonic larvae may reflect contemporary oceanography, while breaks in restricted dispersers reflect historical processes. These results highlight the importance of explicitly considering sampling scale and life history when evaluating phylogeographical patterns.     

Integrating life history traits into predictive phylogeography

Predictive phylogeography seeks to aggregate genetic, environmental and taxonomic data from multiple species in order to make predictions about unsampled taxa using machine‐learning techniques such as Random Forests. To date, organismal trait data have infrequently been incorporated into predictive frameworks due to difficulties inherent to the scoring of trait data across a taxonomically broad set of taxa. We refine predictive frameworks from two North American systems, the inland temperate rainforests of the Pacific Northwest and the Southwestern Arid Lands (SWAL), by incorporating a number of organismal trait variables. Our results indicate that incorporating life history traits as predictor variables improves the performance of the supervised machine‐learning approach to predictive phylogeography, especially for the SWAL system, in which predictions made from only taxonomic and climate variables meets only moderate success. In particular, traits related to reproduction (e.g., reproductive mode; clutch size) and trophic level appear to be particularly informative to the predictive framework. Predictive frameworks offer an important mechanism for integration of organismal trait, environmental data, and genetic data in phylogeographic studies.     

The geological setting of the earliest life forms

Summary Life on Earth may have begun about 4×10⁹ years (4 Ga) ago. Plate tectonics probably operated in the early Archaean, with rapid spreading at mid-ocean ridges, a komatiitic (magnesium-rich) oceanic crust, active volcanic arcs and the development of extensional basins on continental crust. Shallow water environments would have been more restricted and probably shorter-lived than in later geological times; however, extensive shallow seas existed in the later phases of the development of extensional basins. Bacterial communities-presumably photosynthetic-have probably existed in such shallow-water settings and probably at shallow depths in the oceans for at least 3.5 Ga. Because the mid-ocean ridges were probably subaqueous, hydrothermal systems would have been very vigorous and would have offered suitable habitats for early chemo-autotrophic bacterial communities. Early life forms probably also occupied vesicles in lavas, pumice and volcanic breccias, and pores in soft sediments, living in the constant flux of fluid flushing through permeable strata. Other, similar habitats would have existed in volcanic island arcs and in extensional basins.     

A model for the origin of life

Summary A simple statistical model is constructed, describing the transition from disorder to order in a population of mutually catalytic molecules undergoing random mutations. The consequences of the model are calculated, and its possible relevance to the problem of the origin of life is discussed. The main conclusion of the analysis is that the model allows populations of several thousand molecular units to make the transition from disorder to order with reasonable probability.     

动物生活史进化理论研究进展

综述了生活史性状、生活史对策、权衡、适合度及进化种群统计学等动物生活史进化领域的进展。权衡是生活史性状之间相互联系的纽带,分为生理权衡与进化权衡。适合度是相对的,与个体所处的特定环境条件有关,性状进化与适合度之间关系紧密。适合度是生活史进化理论研究的焦点。探讨动物生活史对策的理论很多,影响最大的是MacArthur和Wilson提出的r对策及K对策理论。随年龄的增长,动物存活率及繁殖率逐步下降的过程,称为衰老;解释衰老的进化理论主要有突变-选择平衡假设和多效对抗假设。进化种群统计学将种群统计学应用于生活史进化研究,为探讨表型适合度的进化提供了有效的手段。将进化种群统计学、数量遗传学及特定种系效应理论进行整合,建立完整的动物生活史进化综合理论体系,是当代此领域的最大挑战。     

常见寿命数据类型及生命表的编制方法

生命表是描述种群死亡过程的有用工具,介绍了4种常见的寿命数据类型;寿终数据,右删失数据,左删失数据和区间型数据特征及其相应的数据分析处理方法即生命表法,乘积限估计和Turbull估计法,对生命表法和乘积限估计法应用上的特点进行了比较,同时还对特殊的寿命数据类型－－截断数据做了简要介绍。     

Quality of life issues in relation to the aromatase inhibitor

Maturing data from aromatase inhibitor (AI) trials reveal benefits to many women who might otherwise have relapsed and died from breast cancer. In advanced disease the case for the use of AIs is well established but in the adjuvant and chemoprevention settings some worries about long-term safety remain. Large numbers of women may already be cured by surgery, chemotherapy and radiotherapy making further adjuvant treatment unnecessary. In chemoprevention the ratio of risks to putative benefits remains very unclear, so results from major trials are needed to clarify. When making decisions about treatment women need information about: the available options, likely therapeutic gains, predicted side-effects and convenience of treatment. Adherence is then dependent on the actual burden experienced and impact on QoL. Healthcare professionals often underestimate non-life-threatening but QoL-threatening side-effects, making treatments appear more favorable and acceptable during discussion about therapeutic options. It was hoped that AIs would enhance efficacy without producing unacceptable side-effects that diminish QoL and reduce adherence. Recently published results from the QoL sub-protocols of ATAC, IES and MA-17, looking at anastrozole, exemestane and letrozole, respectively, provide useful indications about the QoL associated with AIs. More information gained from longer-term patient follow-up and preference studies are needed to help clinicians making treatment recommendations and to assist development of ameliorative interventions needed to accompany the most efficacious therapies.     

Prediction of the human life expectancy

We have simulated demographic changes in the human population using the Penna microscopic model, based on the simple Monte Carlo method. The results of simulations have shown that during a few generations changes in the genetic pool of a population are negligible, while improving the methods of compensation of genetic defects or genetically determined proneness to many disorders drastically affects the average life span of organisms. Age distribution and mortality of the simulated populations correspond very well to real demographic data available from different countries. Basing on the comparison of structures of real human populations and the results of simulations it is possible to predict changes in the age structure of populations in the future.     

Phylogenetic relationships and genetic distances between some monostiliferous interstitial nemerteans (Ototyphlonemertes, Hoplonemertea, Nemertea) indicated from the 16s rRNA gene

Part of the 16s rRNA mitochondrial gene is used to reconstruct the relationships within five populations (representing three currently recognized species) of interstitial nemerteans ( Ototyphlonemertes , Hoplonemertea, Nemertea), and to assess genetic divergence between representatives of these populations. The non-helicophoran individuals form a monophyletic sister-group to the helicophoran taxon, which further resolves a previous hypothesis based on morphological characters. The small nucleotide differences between some of the populations are within levels expected for panmictic populations and fail to distinguish them genetically; without applying a phylogenic perspective, some of the populations may be allocated into paraphyletic species assemblages.     

Adaptive evolution of larvae and life cycles

The larval patterns of marine invertebrates pose intriguing questions for both evolutionary and developmental biologists. However, combined investigations have been rare. Quantitative models analyze the selective factors that drive evolutionary change in larval nutrition and timing of metamorphosis. Developmental studies describe the morphogenesis characterizing ancestral and derived larval patterns. Rigorous evolutionary analysis of the transition to derived modes of development is lacking and detailed developmental and ecological data are needed to test and refine theoretical models. A major challenge facing studies of life cycle evolution is the elucidation of the genetic structure and covariance of important developmental and larval traits.     

Driving forces in the origins of life

What were the physico-chemical forces that drove the origins of life? We discuss four major prebiotic ‘discoveries’: persistent sampling of chemical reaction space; sequence-encodable foldable catalysts; assembly of functional pathways; and encapsulation and heritability. We describe how a ‘proteins-first’ world gives plausible mechanisms. We note the importance of hydrophobic and polar compositions of matter in these advances.     

多光子激发技术及其在生命科学中的应用

多光子激发技术是20世纪90年代初发展起来的新技术,其研究和应用前景十分广阔。本文对多光子激发的原理,优缺点以及近年来它的应用领域作了简介。     

Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard

Historical factors, current population size, population connectivity and selective processes at linked loci contribute to shaping contemporary patterns of neutral genetic diversity. It is now widely acknowledged that nuclear and mitochondrial markers react differently to current demography as well as to past history, so the use of both types of markers is often advocated to gain insight on both historical and contemporary processes. We used 12 microsatellite loci genotyped in 13 populations of a mountain lizard (Iberolacerta bonnali) to test whether the historical scenario favoured by a previous mitochondrial study was also supported by nuclear markers and thereby evaluated the consequences of postglacial range movements on nuclear diversity. Congruent signals of recent history were revealed by nuclear and mitochondrial markers using an Approximate Bayesian computation approach, but contemporary patterns of mtDNA and nuclear DNA diversity were radically different. Although dispersal in this species is probably highly restricted at all spatial scales, colonization abilities have been historically good, suggesting capability for reestablishment of locally extinct populations except in fully disconnected habitats.     

Suffering at the end of life

In the end‐of‐life context, alleviation of the suffering of a distressed patient is usually seen as a, if not the, central goal for the medical personnel treating her. Yet it has also been argued that suffering should be seen as a part of good dying. More precisely, it has been maintained that alleviating a dying patient’s suffering can make her unable to take care of practical end‐of‐life matters, deprive her of an opportunity to ask questions about and find meaning in and for her existence, and detach her from reality. In this article, I argue that the aims referred to either do not support suffering or are better served by alleviating it. When the aims would be equally well served by enduring suffering and relieving it, the latter appears to be the preferable option, given that the distress a patient experiences has no positive intrinsic value. Indeed, as the suffering can be very distressing, it may not be worth bearing even if that was the best way to achieve the aims: the distress can sometimes be bad enough to outbalance the worth of achieving the goals. Having considered an objection to the effect that a patient can have a self‐regarding moral duty to endure the distress she faces at the end of life, I conclude that the burden of proof is on the side of those who maintain that the suffering experienced at the end of life ought to be endured as a part of dying well.     

Phylogenetic contrasts and the evolution of mammalian life histories

Summary A recent synthetic model of mammalian life history evolution predicts that M = 3(1–^0.25), where M is the product of age at maturity and the average adult instantaneous mortality rate, and is the ratio of weight at independence to average adult female weight. Previous studies have tested this prediction by fitting a nonlinear regression to data collected for several species of mammals. However, this procedure suffers from non-independence of data points and may have led to incorrect estimates of regression parameters. We test the same life history prediction using phylogenetically independent contrasts with a phylogeny and data for 23 species of mammals. The results accord with the predicted relationship. Our study is one of the few examples where phylogenetic information has been used to improve the statistical power of a quantitative, model-based prediction of how life history variables should co-evolve.     

Serpentinite and the dawn of life

Submarine hydrothermal vents above serpentinite produce chemical potential gradients of aqueous and ionic hydrogen, thus providing a very attractive venue for the origin of life. This environment was most favourable before Earth's massive CO(2) atmosphere was subducted into the mantle, which occurred tens to approximately 100 Myr after the moon-forming impact; thermophile to clement conditions persisted for several million years while atmospheric pCO(2) dropped from approximately 25 bar to below 1 bar. The ocean was weakly acid (pH ～ 6), and a large pH gradient existed for nascent life with pH 9-11 fluids venting from serpentinite on the seafloor. Total CO(2) in water was significant so the vent environment was not carbon limited. Biologically important phosphate and Fe(II) were somewhat soluble during this period, which occurred well before the earliest record of preserved surface rocks approximately 3.8 billion years ago (Ga) when photosynthetic life teemed on the Earth and the oceanic pH was the modern value of approximately 8. Serpentinite existed by 3.9 Ga, but older rocks that might retain evidence of its presence have not been found. Earth's sequesters extensive evidence of Archaean and younger subducted biological material, but has yet to be exploited for the Hadean record.     

哈氏噬纤维菌生活史中形态的变化

【目的】研究哈氏噬纤维菌Cytophaga hutchinsonii 在生活史中细胞形态的变化。【方法】利用光学显微镜、荧光显微镜和电子扫描显微镜对哈氏噬纤维菌生活状态进行详细观察。【结果】发现在饥饿状态下,长杆状菌体开始逐渐弯曲,菌体两端靠近成环形,环形菌体又进一步盘绕收缩成微小球形体,微小球形体在一定条件下能像生孢噬纤维菌的小孢囊一样萌发形成长杆状菌。另外还观察到哈氏噬纤维菌特殊的类核分裂现象。【结论】首次对哈氏噬纤维形成环形菌体和类似小孢囊的微小球形体的过程进行详细描述,为进一步揭示其形态变化与纤维素降解能力之间的关系提供依据。