Defining and evaluating the umbrella species concept for conserving and restoring landscape connectivity.

Conserving or restoring landscape connectivity between patches of breeding habitat is a common strategy to protect threatened species from habitat fragmentation. By managing connectivity for some species, usually charismatic vertebrates, it is often assumed that these species will serve as conservation umbrellas for other species. We tested this assumption by developing a quantitative method to measure overlap in dispersal habitat of 3 threatened species-a bird (the umbrella), a butterfly, and a frog-inhabiting the same fragmented landscape. Dispersal habitat was determined with Circuitscape, which was parameterized with movement data collected for each species. Despite differences in natural history and breeding habitat, we found substantial overlap in the spatial distributions of areas important for dispersal of this suite of taxa. However, the intuitive umbrella species (the bird) did not have the highest overlap with other species in terms of the areas that supported connectivity. Nevertheless, we contend that when there are no irreconcilable differences between the dispersal habitats of species that cohabitate on the landscape, managing for umbrella species can help conserve or restore connectivity simultaneously for multiple threatened species with different habitat requirements.

Spatiotemporal structure of molecular evolution of H5N1 highly pathogenic avian influenza viruses in Vietnam.

BACKGROUND: Vietnam is one of the countries most affected by outbreaks of H5N1 highly pathogenic avian influenza viruses. First identified in Vietnam in poultry in 2001 and in humans in 2004, the virus has since caused 111 cases and 56 deaths in humans. In 2003/2004 H5N1 outbreaks, nearly the entire poultry population of Vietnam was culled. Our earlier study (Wan et al., 2008, PLoS ONE, 3(10): e3462) demonstrated that there have been at least six independent H5N1 introductions into Vietnam and there were nine newly emerged reassortants from 2001 to 2007 in Vietnam. H5N1 viruses in Vietnam cluster distinctly around Hanoi and Ho Chi Minh City. However, the nature of the relationship between genetic divergence and geographic patterns is still unclear. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we hypothesized that genetic distances between H5N1 viruses in Vietnam are correlated with geographic distances, as the result of distinct population and environment patterns along Vietnam's long north to south longitudinal extent. Based on this hypothesis, we combined spatial statistical methods with genetic analytic techniques and explicitly used geographic space to explore genetic evolution of H5N1 highly pathogenic avian influenza viruses at the sub-national scale in Vietnam. Our dataset consisted of 125 influenza viruses (with whole genome sets) isolated in Vietnam from 2003 to 2007. Our results document the significant effect of space and time on genetic evolution and the rise of two regional centers of genetic mixing by 2007. These findings give insight into processes underlying viral evolution and suggest that genetic differentiation is associated with the distance between concentrations of human and poultry populations around Hanoi and Ho Chi Minh City. CONCLUSIONS/SIGNIFICANCE: The results show that genetic evolution of H5N1 viruses in Vietnamese domestic poultry is highly correlated with the location and spread of those viruses in geographic space. This correlation varies by scale, time, and gene, though a classic isolation by distance pattern is observed. This study is the first to characterize the geographic structure of influenza viral evolution at the sub-national scale in Vietnam and can shed light on how H5N1 HPAIVs evolve in certain geographic settings.

Estimating landscape-scale species richness: reconciling frequency- and turnover-based approaches.

One hypothesis for why estimators of species richness tend to underestimate total richness is that they do not explicitly account for increases in species richness due to spatial or environmental turnover in species composition (beta diversity). I analyze the similarity of a data set of native trees in Great Smoky Mountains National Park, USA, and assess the robustness of these estimators against recently developed ones that incorporate turnover explicitly: the total species accumulation method (T-S) and a method based on the distance decay of similarity. I show that the T-S estimator can give reliable estimates of species richness, given an appropriate grouping of sites. The estimator based on distance decay of similarity performed poorly. There are two main reasons for this: sample size effects and the assumption that distance decay of similarity exhibits a power law relationship. I show that estimators based on distance-decay relationships exhibit systematically lower rates of distance decay for samples with few individuals per site independent of environmental variation. Second, the data presented here and many other survey data sets exhibit exponential rather than power law distance-decay relationships. Richness estimators that explicitly incorporate beta diversity can be improved by beginning from an exponential distance-decay relationship and adjusting for the systematic errors introduced by small sample sizes.