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We provide an integrative view of the evolution of dispersal strategies in modern conifers, by characterizing and examining the phylogenetic distribution of diaspore functional morphotypes, diaspore structural compositions, seed coat modifications, and dispersal syndromes using the phylogeny of Leslie et al. (2012). We first classified diaspores into nine functional morphotypes, which represent overall dispersal strategies that encompass the multiple phases of dispersal. We mapped these morphotypes, the eight different structural compositions of diaspores, two types of seed coat modifications, and the four recognized dispersal vectors onto the phylogeny and used maximum parsimony and maximum likelihood to infer ancestral states and assess shifts in dispersal characteristics. We found that structural traits (diaspore composition and seed coat modifications) are more conserved than ecological traits (functional morphotype and dispersal vector/syndrome). Almost all diaspore functional morphotypes have multiple independent origins, with several instances of parallelism (using the same structures to generate a morphotype) within families, but generally functional convergence (using different structures to generate a morphotype) between families. Within extant conifer families, shifts in the dispersal syndrome occur most frequently with simultaneous shifts in both diaspore morphotype and composition. Shifts from winged wind-dispersed to fleshy animal-dispersed diaspores are infrequent and occur only in the direction from wind to animal dispersal. Shifts to gravity or water dispersal occur from both wind and animal dispersed diaspores, concurrent with the loss of dispersal structures from the diaspore. Within both wind and animal-dispersed syndromes, shifts between functional morphotypes represent further differentiation of overall dispersal strategies, and occur most frequently without corresponding changes in the structural composition of the diaspore. The recurrent evolution of distinct functional morphologies suggests that there are local adaptive maxima that balance tradeoffs in traits related to both transport and establishment, within developmental limitations. Overall, our results suggest that the ancestral diaspore type for all modern conifers consisted only of a seed. Conifers diversified in their dispersal strategies through seed coat modifications or by the incorporation of various parts of the seed cone into the diaspore, with the modern conifer families independently evolving their characteristic diaspore compositions. Almost all functional morphotypes were present prior to the Cenozoic in at least one lineage, with more recent shifts in morphotypes representing functional convergence or parallel evolution rather than ecological novelties.

Does evolution proceed faster in larger or smaller populations? The relationship between effective population size (Ne) and the rate of evolution has consequences for our ability to understand and interpret genomic variation, and is central to many aspects of evolution and ecology. Many factors affect the relationship between Ne and the rate of evolution, and recent theoretical and empirical studies have shown some surprising and sometimes counterintuitive results. Some mechanisms tend to make the relationship positive, others negative, and they can act simultaneously. The relationship also depends on whether one is interested in the rate of neutral, adaptive, or deleterious evolution. Here, we synthesize theoretical and empirical approaches to understanding the relationship and highlight areas that remain poorly understood.

Summary The recurrent evolution of convergent forms is a widespread phenomenon in adaptive radiations (e.g., [1–9]). For example, similar ecotypes of anoles lizards have evolved on different islands of the Caribbean [2, 6], benthic-limnetic species pairs of stickleback fish emerged repeatedly in postglacial lakes [1, 3], equivalent sets of spider ecomorphs have arisen on Hawaiian islands [7, 8], and a whole set of convergent species pairs of cichlid fishes evolved in East African Lakes Malawi and Tanganyika [10, 11]. In all these cases, convergent phenotypes originated in geographic isolation from each other. Recent theoretical models, however, predict that convergence should be common within species-rich communities [12, 13], such as species assemblages resulting from adaptive radiations. Here, we present the most extensive quantitative analysis to date of an adaptive radiation of cichlid fishes, discovering multiple instances of convergence in body and trophic morphology. Moreover, we show that convergent morphologies are associated with adaptations to specific habitats and resources and that Lake Tanganyika's cichlid communities are characterized by the sympatric occurrence of convergent forms. This prevalent coexistence of distantly related yet ecomorphologically similar species offers an explanation for the greatly elevated species numbers in cichlid species flocks.

The combination of complete genome sequence information and estimates of mRNA abundances have begun to reveal causes of both silent and protein sequence evolution. Translational selection appears to explain patterns of synonymous codon usage in many prokaryotes as well as a number of eukaryotic model organisms (with the notable exception of vertebrates). Relationships between gene length and codon usage bias, however, remain unexplained. Intriguing correlations between expression patterns and protein divergence suggest some general mechanisms underlying protein evolution.

There have been many wise suggestions of ways that evolution may occur but those ways seem often hard to support with good examples. Viruses have proven to be replete with some of these items. This paper reviews work that shows: (1) very fast rates of evolution; (2) positive Darwinian selection with the selective pressure specifically identified; (3) viral reassortment; (4) grossly unequal rates of evolution depending upon the host of the virus; (5) accurate dating of the cenancestor, the most recent common ancestor; (6) correspondence between the evolutionary tree and the geography of the place of isolation; (7) punctuated molecular evolution; and (8) network evolution.