How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)

Analysing multiple genomic regions while incorporating detection and qualification of discordance among regions has become standard for understanding phylogenetic relationships. In plants, which usually have comparatively large genomes, this is feasible by the combination of reduced-representation library (RRL) methods and high-throughput sequencing enabling the cost effective acquisition of genomic data for thousands of loci from hundreds of samples. One popular RRL method is RADseq. A major disadvantage of established RADseq approaches is the rather short fragment and sequencing range, leading to loci of little individual phylogenetic information. This issue hampers the application of coalescent-based species tree inference. The modified RADseq protocol presented here targets ca. 5,000 loci of 300-600nt length, sequenced with the latest short-read-sequencing (SRS) technology, has the potential to overcome this drawback. To illustrate the advantages of this approach we use the study group Aichryson Webb & Berthelott (Crassulaceae), a plant genus that diversified on the Canary Islands. The data analysis approach used here aims at a careful quality control of the long loci dataset. It involves an informed selection of thresholds for accurate clustering, a thorough exploration of locus properties, such as locus length, coverage and variability, to identify potential biased data and a comparative phylogenetic inference of filtered datasets, accompanied by an evaluation of resulting BS support, gene and site concordance factor values, to improve overall resolution of the resulting phylogenetic trees. The final dataset contains variable loci with an average length of 373nt and facilitates species tree estimation using a coalescent-based summary approach. Additional improvements brought by the approach are critically discussed

Materialismo e primado do objeto em Adorno Materialism e priority of the object on Adorno

Este artigo investiga a "Tese" do primado do objeto na obra de Theodor W. Adorno, central ao seu materialismo não dogmático e relativamente pouco estudada. O primado do objeto será apresentado em seus elementos constitutivos, como crítica ao modo essencialmente idealista da dialética que perpassa o conjunto da obra de Adorno, em especial nos textos e discussões que precederam a publicação da Dialektik der Aufklãrung, para se explicitar no período de elaboração da Negative Dialektik. A "Tese" desenvolve momentos apresentados por Lukács, Benjamin e Horkheimer, particularmente quanto ao nexo entre razão e experiência e se fundamenta especialmente no trajeto Kant - Hegel, como crítica ao idealismo, incorporando de modo estruturante as perspectivas de Marx e de Nietzsche. Ao romper a pretensa "simetria" entre sujeito e objeto, a "Tese" do primado do objeto revela como é insustentável a alegação habermasiana do Discurso filosófico da modernidade segundo a qual Adorno e Horkheimer incidiriam num ceticismo total frente à razão e à sua totalização ideológica. Ao contrário: estes autores, ao articularem de um modo original substância material histórica e argumentação teórica, contribuíram de modo fundamental para examinar o problema da reificação mediante sua relação à objetividade - como o não-idêntico - no âmbito da razão.<br>The thesis of the priority of the object, essential to Adorno's non dogmatic materialism, is analyzed in its constitutive elements, as a criticism of idealism which is present mainly at the works Dialectic of enlightenment and Negative dialectic. As a criticism of idealism, particularly on the relationships between reason and experience as first developed from Kant to Hegel, the thesis is based on Lukács, Benjamin, and Horkheimer contributions and is embedded on the perspectives of Marx and Nietzsche. With its disruption of symmetry between subject and object, the thesis of the priority of the object reveals the frailty of Habermas assertion, in his Philosophical discourse of modernity, of Adorno's and Horkheimer's skepticism towards reason. The present author argues that, in opposition to this claim, Adorno and Horkheimer contributed, with their new way of relating historical material and theoretical approach, to the analysis of the problem of reification in its relations to objectivity - as the non-identical - within the realm of reason, and not outside of it