We improve the taxon sampling for avian phylogeny by analyzing 7 new mitochondrial genomes (a toucan, woodpecker, osprey, forest falcon, American kestrel, heron, and a pelican). This improves inference of the avian tree, and it supports 3 major conclusions. The first is that some birds (including a parrot, a toucan, and an osprey) exhibit a complete duplication of the control region (CR) meaning that there are at least 4 distinct gene orders within birds. However, it appears that there are regions of continued gene conversion between the duplicate CRs, resulting in duplications that can be stable for long evolutionary periods. Because of this stable duplicated state, gene order can eventually either revert to the original order or change to the new gene order. The existence of this stable duplicate state explains how an apparently unlikely event (finding the same novel gene order) can arise multiple times. Although rare genomic changes have theoretical advantages for tree reconstruction, they can be compromised if these apparently rare events have a stable intermediate state. Secondly, the toucan and woodpecker improve the resolution of the 6-way split within Neoaves that has been called an "explosive radiation." An explosive radiation implies that normal microevolutionary events are insufficient to explain the observed macroevolution. By showing the avian tree is, in principle, resolvable, we demonstrate that the radiation of birds is amenable to standard evolutionary analysis. Thirdly, and as expected from theory, additional taxa breaking up long branches stabilize the position of some problematic taxa (like the falcon). In addition, we report that within the birds of prey and allies, we did not find evidence pairing New World vultures with storks or accipitrids (hawks, eagles, and osprey) with Falconids.

Bluehead wrasses undergo dramatic, socially cued female-to-male sex change. We apply transcriptomic and methylome approaches in this wild coral reef fish to identify the primary trigger and subsequent molecular cascade of gonadal metamorphosis. Our data suggest that the environmental stimulus is exerted via the stress axis and that repression of the aromatase gene (encoding the enzyme converting androgens to estrogens) triggers a cascaded collapse of feminizing gene expression and identifies notable sex-specific gene neofunctionalization. Furthermore, sex change involves distinct epigenetic reprogramming and an intermediate state with altered epigenetic machinery expression akin to the early developmental cells of mammals. These findings reveal at a molecular level how a normally committed developmental process remains plastic and is reversed to completely alter organ structures.

Predicting survival and extinction scenarios for climate change requires an understanding of the present day ecological characteristics of species and future available habitats, but also the adaptive potential of species to cope with environmental change. Hybridization is one mechanism that could facilitate this. Here we report statistical evidence that the transfer of genetic information through hybridization is a feature of species from the plant genus Pachycladon that survived the Last Glacial Maximum in geographically separated alpine refugia in New Zealand's South Island. We show that transferred glucosinolate hydrolysis genes also exhibit evidence of intralocus recombination. Such gene exchange and recombination has the potential to alter the chemical defence in the offspring of hybridizing species. We use a mathematical model to show that when hybridization increases the adaptive potential of species, future biodiversity will be best protected by preserving closely related species that hybridize rather than by conserving distantly related species that are genetically isolated. Predicting the response of organisms and estimating loss of genetic diversity are important challenges for evaluating the impact of global climate change on biodiversity 1-3. Although ecological modelling has an important place in understanding this impact 2 , an accurate prediction of range shift and extinction of species also requires determining their adaptive potential, and in particular the frequency with which hybridization facilitates adaptation 4. Determining this is important, because although hybridization can be a maladaptive phenomenon 5 , it might also help species to acquire adaptive traits, respond successfully to environmental change and invade new habitats 1,3,4,6-8. A better understanding of its positive and negative contributions is essential for evaluating biodiversity impacts. Species affected by climate change in the past-the consequences of which are manifested in extant species' ranges and patterns of genetic diversity-provide models to test for signatures of hybridization. Here we studied Pachycladon (Brassicaceae), an allopolyploid genus of 11 species 9 that have radiated in the New Zealand Alps during the Pleistocene period 9,10. Figure 1 shows ice cover at the height of the Last Glacial Maximum (LGM; 21,000-18,000 years ago), the present day distribution of three Pachycladon species, and a chloroplast TCS (statistical parsimony) haplotype network indicating relationships among accessions of the three species. At present, all three species are restricted to greywacke rock in the central and northern regions of the South Island of New

Bluehead wrasses undergo dramatic, socially-cued female to male sex change. We apply transcriptomic and methylome approaches in this wild coral reef fish to identify the primary trigger and subsequent molecular cascade of gonadal metamorphosis.Our data suggest that the environmental stimulus is exerted via the stress axis, that repression of the aromatase gene (encoding the enzyme converting androgens to estrogens) triggers a cascaded collapse of feminizing gene expression, and identifies notable sex-specific gene 2 neofunctionalization. Furthermore, sex change involves distinct epigenetic reprogramming and an intermediate state with altered epigenetic machinery expression akin to the early developmental cells of mammals. These findings reveal at a molecular level how a normally committed developmental process remains plastic and is reversed to completely alter organ structures.