We developed a theoretical framework based on phylogenetic comparative methods to integrate phylogeny into three measures of biodiversity: species variability, richness, and evenness. These metrics can be used in conjunction with permutation procedures to test for phylogenetic community structure. As an illustration, we analyzed data on the composition of 58 lake fish communities in Wisconsin. The fish communities showed phylogenetic underdispersion, with communities more likely to contain closely related species. Using information about differences in environmental characteristics among lakes, we demonstrated that phylogenetic underdispersion in fish communities was associated with environmental factors. For example, lakes with low pH were more likely to contain species in the same clade of acid-tolerant species. Our metrics differ from existing metrics used to calculate phylogenetic community structure, such as net relatedness index and Faith's phylogenetic diversity. Our metrics have the advantage of providing an integrated and easy-to-understand package of phylogenetic measures of species variability, richness, and evenness with well-defined statistical properties. Furthermore, they allow the easy evaluation of contributions of individual species to different aspects of the phylogenetic organization of communities. Therefore, these metrics should aid with the incorporation of phylogenetic information into strategies for understanding biodiversity and its conservation.

Little is known about how density-independent and density-dependent processes affecting population dynamics vary geographically across species' ranges. To address this problem for three vertebrate species (Northern Bobwhite [Colinus virginianus], Ringnecked Pheasants [Phasianus colchicus], and eastern cottontails [Sylvilagus floridanus]), we examined spatially subdivided, long-term (1966-2001), seasonal (January, April, July, and October), time-series data from the Kansas Rural Mail Carrier Survey, USA. All three species have range boundaries in Kansas, with population abundances declining toward the periphery of their ranges. We quantified the strengths of density-dependent and densityindependent processes affecting the dynamics of 10 populations of each species ranging from low (peripheral) to high (central) mean abundance using first-order autoregressive models that incorporate measurement error.For all three species, peripheral populations with lower mean abundance tended to have greater population variability. This pattern could potentially be explained by peripheral regions experiencing either weaker density dependence or greater environmentally driven density-independent fluctuations in per capita population growth rates. In general, density dependence did not vary among geographic regions, although there was a trend for smaller, peripheral populations to exhibit stronger density dependence. Density-independent variability in per capita population growth rates was higher in peripheral populations. Furthermore, density-independent fluctuations in per capita population growth rates were weakly correlated with temperature and precipitation and were highest for the period October through January, identifying fall as the period of greatest environmentally driven variability in population dynamics. Per capita population growth rates fluctuated in moderate synchrony among regions, especially for more abundant, nonperipheral populations in close geographical proximity.The strong density-dependent and stronger density-independent processes in smaller, peripheral populations suggest that the greater variability in peripheral populations' densities is caused by greater population sensitivity to environmental fluctuations. This may make peripheral populations more likely to go extinct and leads to the prediction that, if these species decline to the point of becoming endangered, this decline will be accompanied by a contraction in their geographical ranges.

The northern bobwhite (Colinus virginianus) is an economically important gamebird that is currently undergoing widespread population declines. Despite considerable research on the population ecology of bobwhites, there have been few attempts to model population dynamics of bobwhites to determine the contributions of different demographic parameters to variance of the finite rate of population change (Λ). We conducted a literature review and compiled 405 estimates of 9 demographic parameters from 49 field studies of bobwhites. To identify demographic parameters that might be important for management, we used life‐stage simulation analyses (LSA) to examine sensitivity of Λ to simulated variation in 9 demographic parameters for female bobwhites. In a baseline LSA based on uniform distributions bounded by the range of estimates for each demographic parameter, bobwhite populations were predicted to decline (Λ = 0.56) and winter survival of adults made the greatest contribution to variance of Λ (r2 = 0.453), followed by summer survival of adults (r2 = 0.163), and survival of chicks (r2 = 0.120). Population change was not sensitive to total clutch laid, nest survival, egg hatchability, or 3 parameters associated with the number of nesting attempts (r2<0.06). Our conclusions were robust to alternative simulation scenarios, and parameter rankings changed only if we adjusted the lower bounds of winter survival upwards. Bobwhite populations were not viable with survival rates reported from most field studies. Survival rates may be depressed below sustainable levels by environmental conditions or possibly by impacts of capture and telemetry methods. Overall, our simulation results indicate that management practices that improve seasonal survival rates will have the greatest potential benefit for recovery of declining populations of bobwhites.

Aging is often perceived as a degenerative process caused by random accrual of cellular damage over time. In spite of this, age can be accurately estimated by epigenetic clocks based on DNA methylation profiles from almost any tissue of the body. Since such pan-tissue epigenetic clocks have been successfully developed for several different species, it is difficult to ignore the likelihood that a defined and shared mechanism instead, underlies the aging process. To address this, we generated 10,000 methylation arrays, each profiling up to 37,000 cytosines in highly-conserved stretches of DNA, from over 59 tissue-types derived from 128 mammalian species. From these, we identified and characterized specific cytosines, whose methylation levels change with age across mammalian species. Genes associated with these cytosines are greatly enriched in mammalian developmental processes and implicated in age-associated diseases. From the methylation profiles of these age-related cytosines, we successfully constructed three highly accurate universal mammalian clocks for eutherians, and one universal clock for marsupials. The universal clocks for eutherians are similarly accurate for estimating ages (r>0.96) of any mammalian species and tissue with a single mathematical formula. Collectively, these new observations support the notion that aging is indeed evolutionarily conserved and coupled to developmental processes across all mammalian species - a notion that was long-debated without the benefit of this new and compelling evidence.

Northern bobwhites (Colinus virginianus) are one of the most broadly researched and intensively managed species in North America. However, we argue that a disadvantage of this status is that traditional management principles currently are incompatible with the spatial scale necessary to address the nationwide decline in bobwhite abundance. We maintain that halting or reversing this decline will entail 2 principal changes in the scale of management. Primarily we suggest that habitat oversight must switch from historical fine‐scale management (promotion of edge habitat, weedy fencelines, disked strips, living hedges, and food plots) to regional management of usable space. Secondly, within these regional management areas, we should apply harvest management that employs risk‐sensitive strategies that conservatively avoid undermining the primary goal. This entails narrowing the scale of harvest management from statewide to regional levels. If these ideological changes cannot be made and historical policies remain in force, we risk failing to stabilize, let alone increase, bobwhite populations.

Midwinter waterfowl survey data indicates a long-term decline in the number of wintering American black ducks (Anas rubripes), potentially due to habitat limitations. In order for future estimates of carrying capacity to be determined, it is critical that regional food availability is estimated. We collected pairs of habitat core samples (n ¼ 510) from 5 habitat types in southern New Jersey, USA, during October, January, and April 2006-2008 to estimate resource availability and variability. We collected upper gastrointestinal tracts from hunter-killed birds (n ¼ 45) and late season collections (n ¼ 19) to identify food items and limited our estimates of resource availability to only winter food items; thereby reducing the availability of seed foods found in our core samples by 38% and animal foods by 96%. We did not detect differences in years or sampling period, but did between habitat types. Mudflat habitat had the greatest availability of invertebrate and vertebrate food items and appeared to supply the bulk of energy to black ducks wintering in southern New Jersey. We suggest conservation efforts to be focused on restoring or enhancing mudflat habitat as an integral component of an ecologically functioning salt marsh to increase food availability. ß

Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.

Beyond organisms experiencing direct impacts (mortality) from the presence of anthropogenic features, interactive relationships may exacerbate the effects of anthropogenic disturbance within the context of these features. For example, mortality risk may be affected by the road infrastructure associated with energy development by influencing space use of predators including human hunters. To assess these relationships, we conducted research on northern bobwhite Colinus virginianus across a hunted and non-hunted area of Beaver River Wildlife Management Area, Oklahoma, using radiotelemetry from 2012-2015. We found that bobwhite mortality risk decreased as the distance from primary roads (m) increased across weeks (hazard ratio [HR]  1.008, 95% confidence interval [CI]  1.0003 to 1.0013). The interaction between unit (hunted and non-hunted) and distance from primary roads was not significant (HR  1.00, 95% CI  0.999 to 1.001) indicating that hunting pressure was not a likely explanation for the observed decrease in survival related to primary roads. Bobwhite on the hunted unit avoided exposed soil/sparse vegetation ( β  -0.01, CI  -0.02 to -0.002) and bare ground ( β  -0.01, CI  -0.02 to -0.002) more than bobwhite on the non-hunted unit, however these were weak relationships. No other differences in bobwhite space use were detected related to hunting. Though we were limited to estimating theoretical rather than empirical amounts of hunting pressure during our study, we were unable to detect any negative compounding effects of anthropogenic development and hunting pressure on bobwhite ecology during the hunting season.