分子进化生物学中序列分析方法的新进展

简要介绍了分子进化生物学中序列分析方法的最新进展,特别强调了似然比检验和贝叶斯推论在分子进化和系统发育假说检验中的重要性,并介绍了新方法的一些成功应用,同时还给出了一些重要的信息资源。     

Genomic control for association studies

A dense set of single nucleotide polymorphisms (SNP) covering the genome and an efficient method to assess SNP genotypes are expected to be available in the near future. An outstanding question is how to use these technologies efficiently to identify genes affecting liability to complex disorders. To achieve this goal, we propose a statistical method that has several optimal properties: It can be used with case control data and yet, like family-based designs, controls for population heterogeneity; it is insensitive to the usual violations of model assumptions, such as cases failing to be strictly independent; and, by using Bayesian outlier methods, it circumvents the need for Bonferroni correction for multiple tests, leading to better performance in many settings while still constraining risk for false positives. The performance of our genomic control method is quite good for plausible effects of liability genes, which bodes well for future genetic analyses of complex disorders.     

Choosing between two conflicting scientific hypotheses: The orce dilemmas

How may we choose between conflicting hypotheses when doing a scientific test? Bayesian theory of decision offers a tool to analyse what choosing actually is, preventing us either from giving too much value to rational compounds or from putting aside the scientists’ personal interests and prejudices. Gieres’ cognitive approach to the problem defines the Minimally Open-Minded Scientist’s approach as the right one to dial with the choice dilemma. This approach is used here to give an opinion on the status of the “Orce Man”.     

Do species of Neacratus with anchor-shaped sclerite of endophallus really belong to Neacratus (Coleoptera: Brentidae: Acratini)?

A small group of nine nominal species belonging to the genus Neacratus Alonso-Zarazaga, Lyal, Sforzi & Bartolozzi, 1999 is studied in detail from a morphological point of view. Lectotypes are designated for Brentus obtusus Lund, 1800 and Nemocephalus fulgidus Kleine, 1928. Three new synonymies are proposed: Nemocephalus brevicostatus Kleine, 1922 n. syn. for Brenthus obtusus Lund, 1800, Nemocephalus longiceps Perroud, 1853 n. syn. for Brenthus famulus Boheman, 1840, and Nemocephalus fulgidus Kleine, 1928 n. syn. for B. famulus Boheman, 1840. A new species, Neacratus pascali n. sp., is described from French Guiana. New country records are provided for Neacratus obtusus (Bolivia, Ecuador, French Guiana, Grenada, Peru, Trinidad and Tobago, Venezuela), N. puncticeps (Sharp, 1895) (Colombia, Ecuador, Venezuela), N. guatemalensis (Senna, 1893) (Belize, Colombia, El Salvador), N. deplanatus (Sharp, 1895) (Colombia, Costa Rica, French Guiana, Mexico, Panama, Venezuela) and N. famulus (Paraguay). A phylogenetic analysis carried out on this group shows it forms a monophyletic lineage included in a clade containing most of other species of Neacratus, of which it is the type species; it is therefore not justified to create a new generic name. The possible polyphyletism of the genus Neacratus as a whole and the development of an excessively long rostrum in some male Acratini are discussed.     

Species traits and catchment‐scale habitat factors influence the occurrence of freshwater mussel populations and assemblages

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No substitute for real data: A cautionary note on the use of phylogenies from birth–death polytomy resolvers for downstream comparative analyses

The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth–death polytomy resolver is a method of accounting for phylogenetic uncertainty that places missing (unsampled) taxa onto phylogenetic trees, using taxonomic information alone. Recent studies of birds and mammals have used this approach to generate pseudoposterior distributions of phylogenetic trees that are complete at the species level, even in the absence of genetic data for many species. Many researchers have used these distributions of phylogenies for downstream evolutionary analyses that involve inferences on phenotypic evolution, geography, and community assembly. I demonstrate that the use of phylogenies constructed in this fashion is inappropriate for many questions involving traits. Because species are placed on trees at random with respect to trait values, the birth–death polytomy resolver breaks down natural patterns of trait phylogenetic structure. Inferences based on these trees are predictably and often drastically biased in a direction that depends on the underlying (true) pattern of phylogenetic structure in traits. I illustrate the severity of the phenomenon for both continuous and discrete traits using examples from a global bird phylogeny.