Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon capture to sequence thousands of nuclear loci and complete mitochondrial genomes from closely related chipmunk species in the Tamias quadrivittatus group that are distributed across the Great Basin and the central and southern Rocky Mountains of North America. This recent radiation includes six overlapping, ecologically distinct species (Tamias canipes, Tamias cinereicollis, Tamias dorsalis, T. quadrivittatus, Tamias rufus, and Tamias umbrinus) that show evidence for widespread introgression across species boundaries. Such evidence has historically been derived from a handful of markers, typically focused on mitochondrial loci, to describe patterns of introgression; consequently, the extent of introgression of nuclear genes is less well characterized. We conducted a series of phylogenomic and species-tree analyses to resolve the phylogeny of six species in this group. In addition, we performed several population-genomic analyses to characterize nuclear genomes and infer coancestry among individuals. Furthermore, we used emerging quartets-based approaches to simultaneously infer the species tree (SVDquartets) and identify introgression (HyDe). We found that, in spite of rampant introgression of mitochondrial genomes between some species pairs (and sometimes involving up to three species), there appears to be little to no evidence for nuclear introgression. These findings mirror other genomic results where complete mitochondrial capture has occurred between chipmunk species in the absence of appreciable nuclear gene flow. The underlying causes of recurrent massive cytonuclear discordance remain unresolved in this group but mitochondrial DNA appears highly misleading of population histories as a whole. Collectively, it appears that chipmunk species boundaries are largely impermeable to nuclear gene flow and that hybridization, while pervasive with respect to mtDNA, has likely played a relatively minor role in the evolutionary history of this group. [Cytonuclear discordance; hyridization; introgression, phylogenomics; SVDquartets; Tamias.]

Methylobacterium is one of the most prevalent bacterial genera of the phyllosphere, present on the leaves of nearly every plant. Despite its ubiquity and its importance for host plant function, little is known about whether diversity over space and time within the genus reflects neutral processes like migration and drift, or environmental filtering of life history strategies and adaptations to temperature and host tree species. Here, we investigated how phylogenetic diversity within the genus Methylobacterium is structured by biogeography, seasonality, and growth strategies. Using deep, culture-independent barcoded marker gene sequencing coupled with culture-based approaches, we quantified seasonal shifts in Methylobacterium diversity over a year from early summer to fall in two temperate forests in Quebec, Canada. As an alternative to the 16S rRNA gene, we used rpoB, a highly polymorphic marker gene, which has not experienced detectable horizontal gene transfer nor copy number variation in Methylobacterium genomes. We cultured very different subsets of Methylobacterium diversity from the same leaf, depending upon the temperature of isolation and growth (20 C or 30 C). For instance, one the most abundant Methylobacterium lineages was almost exclusively isolated at 20 C, suggesting long-term adaptation to temperature. Both culture and barcoding approaches revealed that a considerable and previously underestimated diversity of Methylobacterium colonize the surface of leaves in temperate forests. This diversity was strongly structured according to both large (>100km; between forests) and small geographical scales (<1.2km within forests), and among host tree species, and was dynamic over seasonal time scales. To determine if these seasonal effects were driven by temperature, we measured growth of 79 isolates at different temperature treatments. Different lineages showed subtle and significant differences in growth performance when subject to temperature increase or decrease, but most have higher yield and slower growth rate at 20 than 30C, with strong lineage- and season-dependant variation in their overall growth strategies. We proposed that the homogenization of Methylobacterium community structure observed over a growing season resulted from the progressive replacement of isolates with high yield strategy typical of cooperative, structured communities, by isolates with rapid growth. Together our results show how Methylobacterium is phylogenetically structured into lineages with distinct growth strategies, which helps explain their differential abundance across regions, host tree species, and time. This works paves the way for further investigation of adaptive strategies and traits within a ubiquitous phyllosphere genus.

No abstract

Methylobacterium is a group of methylotrophic microbes associated with soil, fresh water, and particularly the phyllosphere, the aerial part of plants that has been well-studied in terms of physiology but whose evolutionary history and taxonomy are unclear. Recent work has suggested that Methylobacterium is much more diverse than thought previously, questioning its status as an ecologically and phylogenetically coherent taxonomic genus. However, taxonomic and evolutionary studies of Methylobacterium have mostly been restricted to model species, often isolated from habitats other than the phyllosphere, and have yet to utilize comprehensive phylogenomic methods to examine gene trees, gene content, or synteny. By analyzing 189 Methylobacterium genomes from a wide range of habitats, including the phyllosphere, we inferred a robust phylogenetic tree while explicitly accounting for the impact of horizontal gene transfer. We showed that Methylobacterium contains four evolutionarily distinct groups of bacteria (namely A, B, C, D), characterized by different genome size, GC content, gene content and genome architecture, revealing the dynamic nature of Methylobacterium genomes. In addition to recovering 59 described species, we identified 45 candidate species, mostly phyllosphere-associated, stressing the significance of plants as a reservoir of Methylobacterium diversity. We inferred an ancient transition from a free-living lifestyle to association with plant roots in Methylobacteriaceae ancestor, followed by phyllosphere association of three of the major groups (A, B, D), whose early branching in Methylobacterium history has been heavily obscured by HGT. Together, our work lays the foundations for a thorough redefinition of Methylobacterium taxonomy, beginning with the abandonment of Methylorubrum.

A central question within the 'new' sociology of knowledge is whether schools act as agencies of transformation or reproduction. Allied to this question is the skeptical claim that schools do not make dramatic differences to children's behaviour, performance, or attitudes in any case. The present ethnographic, grounded theory study, which was located in working class, predominantly Polynesian schools, focusses on these two points and argues that 'successful' schools, through much modified curriculum content, through changed pedagogical techniques and through alternative organisational styles, were endeavouring to effect transformations. However, by contrast, 'unsuccessful' schools were aiming at reproducing existing structures within the community.