The field of molecular plant phylogenetics has had tremendous impacts on botanical studies and taxonomic classification, macroevolution and biogeography, ever since the pioneering studies of Chase et al. (1993) based on DNA sequence data. While those early studies used just a single locus, the plastid gene rbcL, modern studies often employ hundreds to several thousands of genes to infer phylogenetic relationships (e.g.,

Most birds breed in pairs but at least 3% of passerine species are cooperative breeders, whereby more than two adults help to raise the young. The general rarity of cooperative breeding has led to the assumption that cooperative behaviour has evolved from the ancestral trait of pair breeding. However, it has been suggested that pair breeding may be the derived state in some taxa. The primary aim of this research was to test this suggestion using the genus Acanthiza, which contains examples of both cooperatively and pair breeding species. Mitochondrial DNA sequences were used to construct a phylogenetic hypothesis for the tribe containing Acanthiza, the Acanthizini. The breeding behaviour of the species sequenced was determined from records in the literature; where there were no such data the frequency of another social behaviour, flocking, was used as an indicator of breeding behaviour. The mapping of breeding systems onto the phylogeny led to the conclusion that cooperative breeding is the ancestral state in the Acanthizini, with pair breeding evolving twice in the genus Acanthiza. Models explaining the occurrence of cooperative breeding in terms of broad environmental factors or life history do not appear to be applicable to the genus Acanthiza. The pair breeding Acanthiza species cluster into two clades, suggesting some influence of phylogenetic history on the occurrence of the different breeding systems. Combining the results of this study with other data suggests the tendency to breed cooperatively could be ancestral in the superfamily Meliphagoidea.

No abstract

How geographically widespread biological communities assemble remains a major question in ecology. Do parallel population histories allow sustained interactions (such as host-parasite or plant-pollinator) among species, or do discordant histories necessarily interrupt them? Though few empirical data exist, these issues are central to our understanding of multispecies evolutionary dynamics. Here we use hierarchical approximate Bayesian analysis of DNA sequence data for 12 herbivores and 19 parasitoids to reconstruct the assembly of an insect community spanning the Western Palearctic and assess the support for alternative host tracking and ecological sorting hypotheses. We show that assembly occurred primarily by delayed host tracking from a shared eastern origin. Herbivores escaped their enemies for millennia before parasitoid pursuit restored initial associations, with generalist parasitoids no better able to track their hosts than specialists. In contrast, ecological sorting played only a minor role. Substantial turnover in host-parasitoid associations means that coevolution must have been diffuse, probably contributing to the parasitoid generalism seen in this and similar systems. Reintegration of parasitoids after host escape shows these communities to have been unsaturated throughout their history, arguing against major roles for parasitoid niche evolution or competition during community assembly.

Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2–10 MY, yet over 6 kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species. Here we explore the use of larger-scale nuclear gene data obtained though targeted enrichment to increase phylogenetic resolution within Inga. Transcriptome data from three Inga species were used to select 264 nuclear loci for targeted enrichment and sequencing. Following quality control to remove probable paralogs from these sequence data, the final dataset comprised 259,313 bases from 194 loci for 24 accessions representing 22 Inga species and an outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci concatenated or a gene-tree/species-tree approach yielded highly resolved phylogenies. We used coalescent approaches to show that the same targeted enrichment data also have significant power to discriminate among alternative within-species population histories within the widespread species I. umbellifera. In either application, targeted enrichment simplifies the informatics challenge of identifying orthologous loci associated with de novo genome sequencing. We conclude that targeted enrichment provides the large volumes of phylogenetically-informative sequence data required to resolve relationships within recent plant species radiations, both at the species level and for within-species phylogeographic studies.

Relationships among multilocus genetic variation, geography, and environment can reveal how evolutionary processes affect genomes. We examined the evolution of an Australian bird, the eastern yellow robin Eopsaltria australis, using mitochondrial

Coevolutionary models suggest that herbivores drive diversification and community composition in plants. For herbivores, many questions remain regarding how plant defenses shape host choice and community structure. We addressed these questions using the tree genus and its lepidopteran herbivores in the Amazon. We constructed phylogenies for both plants and insects and quantified host associations and plant defenses. We found that similarity in herbivore assemblages between species was correlated with similarity in defenses. There was no correlation with phylogeny, a result consistent with our observations that the expression of defenses in is independent of phylogeny. Furthermore, host defensive traits explained 40% of herbivore community similarity. Analyses at finer taxonomic scales showed that different lepidopteran clades select hosts based on different defenses, suggesting taxon-specific histories of herbivore-host plant interactions. Finally, we compared the phylogeny and defenses of to phylogenies for the major lepidopteran clades. We found that closely related herbivores fed on with similar defenses rather than on closely related plants. Together, these results suggest that plant defenses might be more evolutionarily labile than the herbivore traits related to host association. Hence, there is an apparent asymmetry in the evolutionary interactions between and its herbivores. Although plants may evolve under selection by herbivores, we hypothesize that herbivores may not show coevolutionary adaptations, but instead "chase" hosts based on the herbivore's own traits at the time that they encounter a new host, a pattern more consistent with resource tracking than with the arms race model of coevolution.

Herbaria are unparalleled collections of biodiversity information representing the world's flora. However, this treasure has remained largely inaccessible to genetic studies, frequently limited by the low yields of poor‐quality DNA. Next‐generation sequencing (NGS) has transformed every field of biological research. The different strategies for accessing genetic data using NGS are changing the direction of biodiversity research—we are no longer constrained by a relatively small number of markers for non‐model organisms, by time and cost limited sample sizes, or by incomplete datasets due to recalcitrant DNA extractions or PCR amplification failure. Here we show that targeted enrichment through hybrid capture can be used to generate hundreds of kilobases of nuclear sequence data of the Neotropical genus Inga, from herbarium specimens as old as 180 years and using as little as 16 ng of degraded DNA.