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Mendelian-Mutationism: The Forgotten Evolutionary Synthesis

According to a classical narrative, early geneticists, failing to see how Mendelism provides the missing pieces of Darwin’s theory, rejected gradual changes and advocated an implausible yet briefly popular view of evolution-by-mutation; after decades of delay (in which synthesis was prevented by personal conflicts, disciplinary rivalries, and anti-Darwinian animus), Darwinism ...

Constructive neutral evolution: exploring evolutionary theory’s curious disconnect

found Arlin Stoltzfus's description refreshing and convincing, and I have been a fan of neutral pathways towards complexity ever since. Other earlier writings by Arlin Stoltzfus that I highly enjoyed

Population Diversity of ORFan Genes in Escherichia coli

The origin and evolution of “ORFans” (suspected genes without known relatives) remain unclear. Here, we take advantage of a unique opportunity to examine the population diversity of thousands of ORFans, based on a collection of 35 complete genomes of isolates of Escherichia coli and Shigella (which is included phylogenetically within E. coli). As expected from previous studies, ...

Mutation-Biased Adaptation in a Protein NK Model

Evolutionary trends responsible for systematic differences in genome and proteome composition have been attributed to GC:AT mutation bias in the context of neutral evolution or to selection acting on genome composition. A possibility that has been ignored, presumably because it is part of neither the Modern Synthesis nor the Neutral Theory, is that mutation may impose a directional ...

Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis

Background Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote sharing of data reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. ...

A Sequence-Based Model Accounts Largely for the Relationship of Intron Positions to Protein Structural Features

Claims of intron-structure correlations have played a major role in debates surrounding split gene origins. In the formative (as opposed to disruptive or “insertional”) model of split gene origins, introns represent the scars of chimaeric gene assembly. When analyzed retrospectively, formative introns should tend to fall between modular units, if such units exist, or at least to ...

The Evolutionary Gain of Spliceosomal Introns: Sequence and Phase Preferences

Theories regarding the evolution of spliceosomal introns differ in the extent to which the distribution of introns reflects either a formative role in the evolution of protein-coding genes or the adventitious gain of genetic elements. Here, systematic methods are used to assess the causes of the present-day distribution of introns in 10 families of eukaryotic protein-coding genes ...

Nexplorer: phylogeny-based exploration of sequence family data

Summary: Nexplorer is a web-based program for interactive browsing and manipulation of character data in NEXUS format, well suited for use with alignments and trees representing families of homologous genes or proteins. Users may upload a sequence family dataset, or choose from one of several thousand already available. Nexplorer provides a flexible means to develop customized ...

Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data

Background Evolutionary analysis provides a formal framework for comparative analysis of genomic and other data. In evolutionary analysis, observed data are treated as the terminal states of characters that have evolved (via transitions between states) along the branches of a tree. The NEXUS standard of Maddison, et al. (1997; Syst. Biol. 46: 590–621) provides a portable, ...

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

Background Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great “Tree of Life” (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a ...