Genomic landscape of the global oak phylogeny

The tree of life is highly reticulate, with the history of population divergence buried amongst phylogenies deriving from introgression and lineage sorting. In this study, we test the hypothesis that there are regions of the oak (Quercus, Fagaceae) genome that are broadly informative about phylogeny and investigate global patterns of oak diversity. We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing ca. 250 oak species to infer a time-calibrated phylogeny of the world's oaks. We use reversible-jump MCMC to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20,000 RAD-seq loci back to a recently published oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny. Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification due to climatic transitions or ecological opportunity. The support we find for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome

Beyond the Cut Hunter: A Historical Epidemiology of HIV Beginnings in Central Africa

International audienceIn the absence of direct evidence, an imagined ''cut hunter'' stands in for the index patient of pandemic HIV/AIDS. During the early years of colonial rule, this explanation goes, a hunter was cut or injured from hunting or butchering a chimpanzee infected with simian immunodeficiency virus, resulting in the first sustained human infection with the virus that would emerge as HIV-1M. We argue here that the ''cut hunter'' relies on a historical misunderstanding and ecological oversimplification of human-chimpanzee (Pan Tro-glodytes troglodytes) interactions that facilitated pathogenic transmission. This initial host shift cannot explain the beginnings of the HIV/AIDS pandemic. Instead, we must understand the processes by which the virus became transmissible, possibly between Sangha basin inhabitants and ultimately reached Kinshasa. A historical epidemiology of the late nineteenth and twentieth centuries, provides a much-needed corrective to the major shortcomings of the cut hunter. Based on 62 oral historical interviews conducted in southeastern Cameroon and archival research, we show that HIV emerged from ecological, economic, and socio-political transformations of the late nineteenth and twentieth centuries. The gradual imposition of colonial rule built on and reoriented ecologies and economies, and altered older patterns of mobility and sociality. Certain changes may have contributed to the initial viral host shift, but more importantly, facilitated the adaptation of HIV-1M to human-to-human transmission. Our evidence suggests that the most critical changes occurred after 1920. This argument has important implications for public health policy, underscoring recent work emphasizing alternative pathways for zoonotic spillovers into human beings

Habitat preference of three common fishes for seagrass, Caulerpa taxifolia, and unvegetated substrate in Moreton Bay, Australia

A decrease in seagrass cover and a commensurate increase in Caulerpa taxifolia distribution in Moreton Bay have prompted concern for the impact that habitat change may have on faunal communities. Therefore, it is important to understand the patterns of habitat use. We examined habitat selection of three common seagrass species: double-ended pipefish (Syngnathoides biaculeatus), eastern trumpeter (Pelates quadrilineatus), and fan-bellied leatherjacket (Monacanthus chinensis) using a mesocosm experiment. Fish were given three possible habitat pairings (1) seagrass and C. taxifolia, (2) seagrass and unvegetated, and (3) C. taxifolia and unvegetated. Observation trials were conducted during the day and night over two days. In all trials, fish preferred vegetated habitat (seagrass or C. taxifolia) over unvegetated habitat (sand). In seagrass and C. taxifolia trials, all species preferred seagrass significantly over C. taxifolia. Habitat use patterns did not differ between day and night trials. Caulerpa taxifolia provides a valuable structured habitat in the absence of seagrass; however, it is unclear if C. taxifolia meadows provide other resource benefits to fishes beyond that of shelter

Changes in Seagrass Species Composition in Northwestern Gulf of Mexico Estuaries: Effects on Associated Seagrass Fauna

The objective of this study was to measure the communities associated with different seagrass species to predict how shifts in seagrass species composition may affect associated fauna. In the northwestern Gulf of Mexico, coverage of the historically dominant shoal grass (Halodule wrightii) is decreasing, while coverage of manatee grass (Syringodium filiforme) and turtle grass (Thalassia testudinum) is increasing. We conducted a survey of fishes, crabs, and shrimp in monospecific beds of shoal, manatee, and turtle grass habitats of South Texas, USA to assess how changes in sea grass species composition would affect associated fauna. We measured seagrass parameters including shoot density, above ground biomass, epiphyte type, and epiphyte abundance to investigate relationships between faunal abundance and these seagrass parameters. We observed significant differences in communities among three seagrass species, even though these organisms are highly motile and could easily travel among the different seagrasses. Results showed species specific relationships among several different characteristics of the seagrass community and individual species abundance. More work is needed to discern the drivers of the complex relationships between individual seagrass species and their associated fauna