Who is the closest extant cousin of humans? Total‐evidence approach to hominid phylogenetics via simultaneous optimization

J. R. Grehan & J. H. Schwartz (Journal of Biogeography, 2009, 36 , 1823–1844) argued that humans (Homo) are more closely related to orangutans (Pongo) than to chimpanzees (Pan), and used this scenario to draw biogeographical conclusions about human origins. They discussed a contradiction between phenotypical and molecular results that has led to a debate about the reliability of genetic versus phenotypic data. The main aim of our study is to test the conflicting phylogenetic hypotheses by a total‐evidence analysis based on simultaneous optimization of extensive phenotypic and molecular data sets. Our results supported the human–chimpanzee clade, without any phenotypical–molecular data conflict, as the same phylogeny emerged both from the total analysis and when the molecular and phenotypic data were analysed separately. Sensitivity analyses showed that the result was not dependent on the parameters chosen for character weighting.     

Status of the South American tuberous legume Pachyrhizus tuberosus (Lam.) Spreng.: Field observations, taxonomic analysis, linguistic studies and agronomic data on the diversity of the South American Pachyrhizus tuberosus (Lam.) Spreng. complex with special reference to the identification of two new cultivar groups from Ecuador and Peru

The tuberous legume Pachyrhizus tuberosus is found in cultivation sporadically throughout the tropical lowlands of South America. As a result of field studies conducted in Bolivia, Ecuador, Peru and Venezuela, three distinct cultivar groups have been identified. Rare references presenting further evidence in support of this grouping, and yielding information on the cultivation history, are reviewed. The differences in morphology, agricultural practices, tuberous root quality and uses have been studied, as has the linguistic evidence of the origin and domestication processes. The herbarium and live material have been subjected to multivariate analyses in order to establish which easily observable phenotypic characters can be used in the identification of the three cultivar groups. This paper reports on the analysis of 23 morphological characteristics from 31 P. tuberosus cultivar records. The considerable potential of this cultivar/landrace complex and the possibilities of establishing in situ conservation initiatives are discussed. This revised version was published online in August 2006 with corrections to the Cover Date.     

Phylogenetic Relationships of Extinct Cetartiodactyls: Results of Simultaneous Analyses of Molecular, Morphological, and Stratigraphic Data

Although some recent morphological and molecular studies agree that Cetacea is closely related to Hippopotamidae, there is little consensus on the phylogeny within Cetartiodactyla. We addressed this problem by conducting two analyses: (1) a simultaneous cladistic analysis of intrinsic data (morphology and molecules) and (2) a stratocladistic analysis, which included morphological, molecular, and stratigraphic data. Unlike previous simultaneous analyses, we had the opportunity to include data from the recently described hindlimbs of protocetid and pakicetid cetaceans. Our intrinsic dataset includes 73 taxa scored for 8,229 informative characters, of which 208 are morphological and 8,021 molecular. Both analyses supported the exclusion of Mesonychia from Cetartiodactyla and a close phylogenetic relationship between Hippopotamidae and Cetacea. Many polytomies in the strict consensus of the most parsimonious trees for the intrinsic dataset can be attributed to differing positions for Raoellidae, which in some trees is the sister-group to Cetacea. Pruning Raoellidae and 18 other taxa from all most parsimonious produced a fully resolved agreement subtree, which indicates that the Old World taxa Cebochoerus and Mixtotherium are successive stem taxa to Whippomorpha (i.e., Cetacea + Hippopotamidae). The main result of adding stratigraphic information to the intrinsic dataset was that we found fewer most parsimonious trees, which in most respects were congruent with a subset of the shortest trees for the intrinsic dataset. Our stratocladistic analysis supports species of Diacodexis as the most basal cetartiodactyls, a clade of suiform cetartiodactyls, a monophyletic Tylopoda that includes Protoceratidae, and a monophyletic Carnivora. We were unable to identify any pre-Miocene stem taxa to Hippopotamidae, thus its ghost lineage is still 39 million years long. The relatively low Bremer support for many nodes in our trees indicates that our phylogenetic hypotheses should be subjected to further testing.     

On the Even Greater Need for Precaution Under Global Change

The greater the potential for disastrous, large-scale, or catastrophic impacts on health, the greater the case for precaution. The imperative for precautionary action, critical also for downstream determinants of health, is at least as compelling where macro-level concerns about the sustainability of life on Earth are at issue. In this context, I propose that a higher threshold of uncertainty is needed where large-scale harms to health and well-being are possible. Initial efforts must focus on the training of researchers and risk managers for competencies in complexity, and in systems approaches to transdisciplinary enquiry. Revisiting the intent behind Bradford Hill on causation is an essential first step. Focus on the more proximate causes of diseases, such as those related either to occupational exposures or to more downstream environmental exposures, is left to others in this collection.     

Microbial DNA profiling by multiplex terminal restriction fragment length polymorphism for forensic comparison of soil and the influence of sample condition

Aims:  To evaluate: (i) the impact of air-drying on bacterial, archaeal and fungal soil DNA profiles and (ii) the potential use of multiplex-terminal restriction fragment length polymorphism (M-TRFLP) as a tool for forensic comparison of soil.
Methods and Results:  An M-TRFLP approach was used to profile bacterial, archaeal and fungal DNA profiles from five different soil sites. Air-drying soil significantly reduced the quantity of DNA but the number of operational taxanomic units (OTU) was unaffected. The impact of air-drying on soil DNA profiles was dependent on soil site and microbial primers. Fungal profiles were altered the least by air-drying. For prokaryotic profiles, air-drying altered the relative similarity/dissimilarity between soil sites. The M-TRFLP approach was more discriminatory compared with soil colour and single-taxa profiling, but did not significantly improve resolution between two similar soils.
Conclusions:  Of those tested, soil fungi were potentially the more robust target for application to soil forensic studies as they were altered less by air-drying and provided clear discrimination of soils from different sites. The M-TRFLP method demonstrated potential to achieve greater resolution, discriminating the soil sites based on both bacterial and fungal components.
Significance and Impact of the Study:  Soil DNA profiling has potential as a forensic tool, but sample condition and the appropriate selection of microbial target taxa must be considered.     

Weight of the Evidence Evaluation of Low-Dose Reproductive and Developmental Effects of Bisphenol A

A panel convened by the Harvard Center for Risk Analysis (HCRA) evaluated the weight of evidence for potential developmental and reproductive toxicity of bisphenol A (BPA, CASRN 80-05-7) in animals at doses well below the Lowest Observed Adverse Effect Level (LOAEL) of 50 mg/kg-day previously identified by the U.S. Environmental Protection Agency (US EPA) and even US EPA's reference dose (RfD) of 0.05 mg/kg-day. The effects are hypothesized to occur through an endocrine-modulating mode of action, specifically through estrogen receptors. The panel focused on potential male reproductive effects but also examined other endpoints possibly associated with hormone-like effects. The review considered studies published through April 2002. A formal deliberation framework focused on consistency, generalizability, and biological plausibility. The panel found no consistent affirmative evidence of low-dose BPA effects for any endpoint. Inconsistent responses across rodent species and strains made generalizability of low-dose BPA effects questionable. Lack of adverse effects in two multiple-generation reproductive and developmental studies casts doubt on suggestions of significant physiological or functional impairment. The panel was concerned about generalization of non-oral administration results to oral exposures. Differences in the pattern of BPA responses compared to estradiol or diethylstilbestrol (DES) cast doubt on estrogenicity as a low-dose mechanism of action for BPA. Finally, there is indirect evidence that humans may be less sensitive to possible estrogenic effects from BPA exposure due to pharmacodynamic factors. The panel recommended replication of existing studies under carefully controlled conditions and further study of BPA's pharmacokinetics and pharmacodynamics. The study was funded by a grant from the American Plastics Council.     

不同亲子鉴定试剂盒对D7S820基因座稀有等位基因检测结果比较

目的：观察分析用不同亲子鉴定试剂盒对D7S820基因座稀有等位基因检测结果的差异。方法：280名不同个体的血样DNA提取和基因型检测,按中华人民共和国公共安全行业标准GA／T382—2002和GA／T383—2002进行;分别用Identifiler试剂盒（美国AB公司）、PowerPlex 18Dsystem试剂盒（美国普洛麦格公司）、GoldeneyeTM20A试剂盒（北京基点认知技术有限公司）,经PCR复合扩增STR基因座,用AB公司DNA序列分析仪电泳分离扩增产物和激光扫描分析。结果：检测到280名不同个体的常用常染色体STR基因座的等位基因。,其中六份样本在D7S820基因座上,Identifiler试剂盒检测的基因型与PowerPlex 18D—system和GoldeneyeTM20A试剂盒检测的基因型结果有差异。结论：不同厂家生产的试剂盒检测常用常染色体D7S820基因座的稀有等位基因存在有一定误差。