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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.

Comparison of mitochondrial and morphological divergence in eight populations of a widespread leaf-litter skink is used to determine the relative importance of geographic isolation and natural selection in generating phenotypic diversity in the Wet Tropics Rainforest region of Australia. The populations occur in two geographically isolated regions, and within each region, in two different habitats (closed rainforest and tall open forest) that span a well characterized ecological gradient. Morphological differences among ancient geographic isolates (separated for several million years, judging by their mitochondrial DNA sequence divergence) were slight, but morphological and life history differences among habitats were large and occurred despite moderate to high levels of mitochondrial gene flow. A field experiment identified avian predation as one potential agent of natural selection. These results indicate that natural selection operating across ecological gradients can be more important than geographic isolation in similar habitats in generating phenotypic diversity. In addition, our results indicate that selection is sufficiently strong to overcome the homogenizing effects of gene flow, a necessary first step toward speciation in continuously distributed populations. Because ecological gradients may be a source of evolutionary novelty, and perhaps new species, their conservation warrants greater attention. This is particularly true in tropical regions, where most reserves do not include ecological gradients and transitional habitats.

Riparian habitats typically support high diversity and density of both plants and animals. With the dramatic loss of riparian habitats, restoring them has become a priority among conservation practitioners. Diversity and density of avian species tend to increase following riparian restoration, but little is known about how restored habitats function to meet particular species' needs. Habitat structure is an important factor affecting species diversity and density and can influence nest-site selection and reproductive success. To evaluate habitat restoration, we examined interactions between habitat structure, nest-site selection, and nesting success in Song Sparrows (Melospiza melodia) nesting in restored, mature, and young naturally regenerating stands of riparian forest. We found that stand types differed markedly in structure, and that habitat structure influenced both nest-site selection and rates of nest loss to predation. Comparison of habitat structure among the three stand types indicated that restored stands offered fewer acceptable nest sites and poorer protection from nest predation. Concordant with those differences in habitat structure, Song Sparrows showed trends toward less density in restored stands than in mature forest, and had poorer nesting success as a result of predation.

We studied Song Sparrow (Melospiza melodia) reproductive ecology in natural and restored riparian forest to evaluate the influence of habitat structure and nest-site selection on parasitism by Brown-headed Cowbirds (Molothrus ater). Logistic regression revealed that habitat structure affected the probability of parasitism at two scales, BROAD (within 11.3 m of the nest) and LOCAL (within 5 m of the nest). Nests with abundant lateral cover at a height of < 1 m (BROAD) were less likely to be parasitized, suggesting that lateral cover at ground level may reduce parasitism by concealing host movements in the vicinity of the nest. In contrast, nests with abundant foliage cover at a height of 2-3 m (LOCAL) were more likely to be parasitized, suggesting that foliage cover above the nest may increase parasitism by providing perches from which female cowbirds can watch host activities and find nests. Sparrow nest-site selection varied among forest types, but lateral cover at ground level and foliage cover above the nest were similar for nests in each forest type. Results suggest that further research on the effects of habitat structure on nest-site selection and cowbird parasitism could lead to methods of reducing parasitism through appropriate habitat management and restoration efforts.

Riparian habitats typically support high diversity and density of both plants and animals. With the dramatic loss of riparian habitats, restoring them has become a priority among conservation practitioners. Diversity and density of avian species tend to increase following riparian restoration, but little is known about how restored habitats function to meet particular species' needs. Habitat structure is an important factor affecting species diversity and density and can influence nest-site selection and reproductive success. To evaluate habitat restoration, we examined interactions between habitat structure, nest-site selection, and nesting success in Song Sparrows (Melospiza melodia) nesting in restored, mature, and young naturally regenerating stands of riparian forest. We found that stand types differed markedly in structure, and that habitat structure influenced both nest-site selection and rates of nest loss to predation. Comparison of habitat structure among the three stand types indicated that restored stands offered fewer acceptable nest sites and poorer protection from nest predation. Concordant with those differences in habitat structure, Song Sparrows showed trends toward less density in restored stands than in mature forest, and had poorer nesting success as a result of predation.

Maximum lifespan of a species is the oldest that individuals can survive, reflecting the genetic limit of longevity in an ideal environment. Here we report methylation-based models that accurately predict maximum lifespan (r=0.89), gestational time (r=0.96), and age at sexual maturity (r=0.87), using cytosine methylation patterns collected from over 12,000 samples derived from 192 mammalian species. Our epigenetic maximum lifespan predictor corroborated the extended lifespan in growth hormone receptor knockout mice and rapamycin treated mice. Across dog breeds, epigenetic maximum lifespan correlates positively with breed lifespan but negatively with breed size. Lifespan-related cytosines are located in transcriptional regulatory regions, such as bivalent chromatin promoters and polycomb-repressed regions, which were hypomethylated in long-lived species. The epigenetic estimators of maximum lifespan and other life history traits will be useful for characterizing understudied species and for identifying interventions that extend lifespan.

The presence of effusion/empyema in pediatric pneumonia can increase treatment complexity by possibly requiring pleural drainage. Currently, no data support the superiority of any drainage modalities in children. We performed a retrospective cohort study using the Pediatric Health Information System database from 2003 to 2008. A total of 14,936 children were hospitalized with effusion/empyema. Fifty-two percent of children were treated with antibiotics alone. Compared with patients receiving a chest tube, patients receiving antibiotics alone, thoracotomy, and video-assisted thoracoscopic surgery had a shorter length of stay, lower mortality rates, and fewer re-interventions. Delaying drainage by 1 to 3 days was associated with a lower mortality rate, and a delay of more than 7 days was associated with a higher mortality rate. Half of all children with effusion/empyema are treated with antibiotics alone with low morbidity and mortality. Initial video-assisted thoracoscopic surgery or thoracotomy had improved outcomes compared with other interventions. Intervention should not be delayed beyond 7 days.

Preserving biodiversity under rapidly changing climate conditions is challenging. One approach for estimating impacts and their magnitude is to model current relationships between genomic and environmental data and then to forecast those relationships under future climate scenarios. In this way, understanding future genomic and environmental relationships can help guide management decisions, such as where to establish new protected areas where populations might be buffered from high temperatures or major changes in rainfall. However, climate warming is only one of many anthropogenic threats one must consider in rapidly developing parts of the world. In Central Africa, deforestation, mining, and infrastructure development are accelerating population declines of rainforest species. Here we investigate multiple anthropogenic threats in a Central African rainforest songbird, the little greenbul (Andropadus virens). We examine current climate and genomic variation in order to explore the association between genome and environment under future climate conditions. Specifically, we estimate Genomic Vulnerability, defined as the mismatch between current and predicted future genomic variation based on genotype–environment relationships modeled across contemporary populations. We do so while considering other anthropogenic impacts. We find that coastal and central Cameroon populations will require the greatest shifts in adaptive genomic variation, because both climate and land use in these areas are predicted to change dramatically. In contrast, in the more northern forest–savanna ecotones, genomic shifts required to keep pace with climate will be more moderate, and other anthropogenic impacts are expected to be comparatively low in magnitude. While an analysis of diverse taxa will be necessary for making comprehensive conservation decisions, the species‐specific results presented illustrate how evolutionary genomics and other anthropogenic threats may be mapped and used to inform mitigation efforts. To this end, we present an integrated conceptual model demonstrating how the approach for a single species can be expanded to many taxonomically diverse species.

Effective conservation and management of threatened wildlife populations require an accurate assessment of age structure to estimate demographic trends and population viability. Epigenetic aging models are promising developments because they estimate individual age with high accuracy, accurately predict age in related species, and do not require invasive sampling or intensive long-term studies. Using blood and biopsy samples from known age plains zebras (Equus quagga), we model epigenetic aging using two approaches: the epigenetic clock (EC) and the epigenetic pacemaker (EPM). The plains zebra EC has the potential for broad application within the genus Equus given that five of the seven extant wild species of the genus are threatened. We test the EC’s ability to predict age in sister taxa, including two endangered species and the more distantly related domestic horse, demonstrating high accuracy in all cases. By comparing chronological and estimated age in plains zebras, we investigate age acceleration as a proxy of health status. An interaction between chronological age and inbreeding is associated with age acceleration estimated by the EPM, suggesting a cumulative effect of inbreeding on biological aging throughout life.Larison et al. report epigenetic aging models in plains zebras (Equus quagga) using the epigenetic clock and epigenetic pacemaker approaches. Their epigenetic clock allows age to be accurately estimated in endangered sister species, and the pacemaker model identifies an association between inbreeding and accelerating aging.