A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.     

A nonparametric procedure for the two-factor mixed model with missing data

We develop a nonparametric imputation technique to test for the treatment effects in a nonparametric two-factor mixed model with incomplete data. Within each block, an arbitrary covariance structure of the repeated measurements is assumed without the explicit parametrization of the joint multivariate distribution. The number of repeated measurements is uniformly bounded whereas the number of blocks tends to infinity. The essential idea of the nonparametric imputation is to replace the unknown indicator functions of pairwise comparisons by the corresponding empirical distribution functions. The proposed nonparametric imputation method holds valid under the missing completely at random (MCAR) mechanism. We apply the nonparametric imputation on Brunner and Dette's method for the nonparametric two-factor mixed model and this extension results in a weighted partial rank transform statistic. Asymptotic relative efficiency of the nonparametric imputation method with the complete data versus the incomplete data is derived to quantify the efficiency loss due to the missing data. Monte Carlo simulation studies are conducted to demonstrate the validity and power of the proposed method in comparison with other existing methods. A migraine severity score data set is analyzed to demonstrate the application of the proposed method in the analysis of missing data.     

Cholesterol and Clioquinol modulation of Aβ(1-42) interaction with phospholipid bilayers and metals

The β-sheet plaques that are the most obvious pathological feature of Alzheimer's disease are composed of amyloid-β peptides and are highly enriched in the metal ions Zn, Fe and Cu. The interaction of the full-length amyloid peptide, Aβ(1-42), with phospholipid lipid bilayers was studied in the presence of the metal-chelating drug, Clioquinol (CQ). The effect of cholesterol and metal ions was also determined using solid-state ³¹P and ²H NMR. CQ modulated the effect of metal ions on the integrity of the bilayer and although CQ perturbed the phospholipid membrane, the bilayer integrity was maintained. Model membranes enriched in cholesterol were studied under conditions of peptide association and incorporation. Solid-state NMR showed that the bilayer integrity was preserved in cholesterol-enriched membranes in comparison to phosphatidylcholine-phosphatidylserine bilayers. Changes in peptide structure, consistent with an increase in β-sheet, were observed using specifically ¹³C-labelled Aβ(1-42) by magic angle spinning NMR. Results using aligned phosphatidylcholine bilayers and completely ¹⁵N-labelled peptide indicated that the peptide aggregated. The results are consistent with oligomeric β-sheet structured peptides only partially penetrating the bilayer and cholesterol reducing the membrane disruption.     

Problems in polychaete systematics

Some of the intriguing issues in current polychaete systematics are reviewed. (1) The root of the `polychaete' tree. Currently there are two major hypotheses concerning the root position among polychaetes. One is based on rooting cladograms with outgroups such as Mollusca and result in simple-bodied taxa such as Opheliidae and Questidae forming a basal annelid grade along with Clitellata. Other hypotheses do not use outgroup rooting but involve scenarios on the evolution of the group and would place taxa in Aciculata as basal annelids, thus making Aciculata and Phyllodocida paraphyletic. Molecular sequence data has been of little help in resolving this issue thus far, largely due to limited taxon sampling. (2) Paraphyly. Owing, in part, to a tradition involving the emphasis on differences among taxa, and the application of Linnean ranks (e.g., family), paraphyly is undoubtedly a widespread phenomenon in polychaete systematics. An example of this has been proposed already for Spionidae. If the tree topology and rooting used by Blake & Arnofsky (1999) is correct, Spionidae is made paraphyletic by the recognition of the following four family-ranked taxa; Trochochaetidae, Poecilochaetidae, Longosomatidae and Uncispionidae. Another possible example is seen with Cirratulidae. A preliminary cladistic analysis shows that it is entirely possible that seven other taxa recognised as families may be nested within Cirratulidae. These include Acrocirridae, Ctenodrilidae, Fauveliopsidae, Flabelligeridae, Flotidae, Poeobiidae and Sternaspidae. (3) Problematic taxa. Apart from the problems exposed by the analysis of Cirratuliformia, the position of some of these groups, such as Aberranta, Alciopidae, Hesionides,Lopadorhynchidae, Microphthalmus,Nerillidae, Spinther,Tomopteridae and Sabellariidae, is discussed.     

三维取向PLGA神经导管促进坐骨神经再生的实验研究

目的：探讨应用改进静电纺丝技术一次成型制备三维（3D）取向聚乳酸与聚羟基乙酸共聚物（PLGA）纳米神经导管的可行性,检测其对坐骨神经再生的促进作用。方法：应用改进的静电纺丝技术制备无缝取向PLGA纳米神经导管,通过扫描电镜和透射电镜检测支架的纳米结构;分别制备取向和非取向纳米纤维支架修复13mm坐骨神经缺损模型。36只成年SD大鼠随机分为3组（每组12只）,A组：非取向PLGA神经导管组（阴性对照）;B组：取向PLGA神经导管组,C组：自体神经移植组（阳性对照）,于术后3月通过大体观察、行走足印分析、腓肠肌萎缩率、电生理检测、组织形态学检测、透射电镜检测及图像分析,评价无缝取向PLGA纳米神经导管修复坐骨神经缺损的效果。结果：神经导管修复神经缺损三月后,大体观察显示神经导管结构完整,无坍塌和断裂;各组再生神经均有通过神经导管长入远端。B组与C组的腓肠肌萎缩率和神经电传导速度无统计学差异（P〈0.05）,均优于A组。B组与C组再生神经纤维数量及成熟程度均要明显优于A组。结论：无缝取向PLGA纳米神经导管能够诱导并促进神经再生,提高坐骨神经再生的质量,有望成为自体神经移植的替代物。     

铁线莲属研究随记(Ⅱ)

(1)对铁线链属以下诸种Clematis potaninii Maxim., C．heynei Rau,C．trichotoma Nakai,C．apiculata Hook．f.&; Thoms., C．theobromina Dunn,C．hedysarifolia DC．和C．dissecta Baker的系统位置进行了讨论,提出了新见解;(2)过去一些作者或不承认C．trifida Hook．,C．pimpinellifolia Hook.,C．oligophylla Hook．,和Clematopsis lineariloba Hutch诸种,或进行降级,作为种下分类群处理。本文作者在研究了有关标本之后认为上述4种有明显区别特征,均应成立;(3)对裂叶铁线莲Clematis parviloba Gardn．&; Champ．的5个变种,短毛铁线莲C．puberula Hook．f.&; Thoms．的4个变种和丝铁线莲组sect．Naraveliopsis Hand.-Mazz．的20个种做出新的分类安排;(4)归并了subsect．Potanimianae W．T．Wang,C．heynei M．Johnson,C．petelotii Gagnep．以及其他几个学名;(5)描述了2新亚组,4新系,3新种和3新变种;(6)做出了3个新等级,4个新组合。     

三维取向PLGA神经导管促进坐骨神经再生的实验研究

目的:探讨应用改进静电纺丝技术一次成型制备三维(3D)取向聚乳酸与聚羟基乙酸共聚物(PLGA)纳米神经导管的可行性,检测其对坐骨神经再生的促进作用。方法:应用改进的静电纺丝技术制备无缝取向PLGA纳米神经导管,通过扫描电镜和透射电镜检测支架的纳米结构;分别制备取向和非取向纳米纤维支架修复13mm坐骨神经缺损模型。36只成年SD大鼠随机分为3组(每组12只),A组:非取向PLGA神经导管组(阴性对照);B组:取向PLGA神经导管组,C组:自体神经移植组(阳性对照),于术后3月通过大体观察、行走足印分析、腓肠肌萎缩率、电生理检测、组织形态学检测、透射电镜检测及图像分析,评价无缝取向PLGA纳米神经导管修复坐骨神经缺损的效果。结果:神经导管修复神经缺损三月后,大体观察显示神经导管结构完整,无坍塌和断裂;各组再生神经均有通过神经导管长入远端。B组与C组的腓肠肌萎缩率和神经电传导速度无统计学差异(P0.05),均优于A组。B组与C组再生神经纤维数量及成熟程度均要明显优于A组。结论:无缝取向PLGA纳米神经导管能够诱导并促进神经再生,提高坐骨神经再生的质量,有望成为自体神经移植的替代物。     

Taxonomic surrogacy in biodiversity assessments,and the meaning of Linnaean ranks

The majority of biodiversity assessments use species as the base unit. Recently, a series of studies have suggested replacing numbers of species with higher ranked taxa (genera, families, etc.); a method known as taxonomic surrogacy that has an important potential to save time and resources in assesments of biological diversity. We examine the relationships between taxa and ranks, and suggest that species/higher taxon exchanges are founded on misconceptions about the properties of Linnaean classification. Rank allocations in current classifications constitute a heterogeneous mixture of various historical and contemporary views. Even if all taxa were monophyletic, those referred to the same rank would simply denote separate clades without further equivalence. We conclude that they are no more comparable than any other, non‐nested taxa, such as, for example, the genus Rattus and the phylum Arthropoda, and that taxonomic surrogacy lacks justification. These problems are also illustrated with data of polychaetous annelid worms from a broad‐scale study of benthic biodiversity and species distributions in the Irish Sea. A recent consensus phylogeny for polychaetes is used to provide three different family‐level classifications of polychaetes. We use families as a surrogate for species, and present Shannon‐Wiener diversity indices for the different sites and the three different classifications, showing how the diversity measures rely on subjective rank allocations.     

Food access in captive Ammotragus: the role played by hierarchy and mother–infant interactions

An analysis of individuals' behavior when accessing a restricted food source (troughs) was carried out in a captive population of aoudad (Ammotragus lervia). Access to the troughs followed a strict hierarchical order, as higher‐ranking individuals fed before lower‐ranking ones. Unweaned male and female calves made use of the troughs from the ages of 2 and 3 months, respectively. Both fed from the troughs more frequently and for longer periods when their mother was present, which allowed them to make use of the troughs while skipping the hierarchical order. Calves received fewer threats when in proximity to their mothers, particularly in high‐ranking families. Mothers defended their calves from other herdmates more frequently when at the feeding area than in other areas of the herd. However, only sated mothers let their calves feed freely from the troughs; unsated mothers showed an aggressive behavior even toward their calves. I conclude that a maternal presence is necessary for aoudad calves to successfully feed from troughs, and that families of higher social rank benefit by getting access to this food source earlier in the day and are disturbed less than low‐ranking families. Zoo Biol 21:597–605, 2002. © 2002 Wiley‐Liss, Inc.