Additional file 5: Comparison of microsatellite- and SNP-based genetic variation.

Additional file 2: Summary statistics associated with nuclear genome sequencing, assembly and annotation.

Natural enemies have been implicated as agents of negative density dependence (NDD) in tropical forests, but their relative contributions to NDD, and thus to the maintenance of diversity, are largely unknown. We monitored the rates of survival and relative growth rates on seedlings for ten years in tropical moist forest in Manu National Park, Peru. We then experimentally manipulated the plots to exclude fungal pathogens, insects, small mammals, and large mammals for an additional 31...

Although amphibians use human-created habitats in urban landscapes, few studies have investigated the quality of these habitats. To assess habitat quality of stormwater management ponds and adjacent urban uplands forwood frogs (Lithobates sylvaticus) and American toads (Anaxyrus americanus), we compared life history characteristics between populations breeding across an urbanization gradient. Specifically, we compared body size, ages of breeding adults, and female reproductive investment among urban, suburban, and rural populations in Baltimore County, Maryland, USA. Although...

Humans exhibit a high level of vocal plasticity in speech production which allows us to acquire both native and foreign languages, dialects and adapt to local accents in social communication. In comparison, non-human primates exhibit limited vocal plasticity, especially in adulthood, which would limit their ability to adapt to different social and environmental contexts in vocal communication. Here we quantitatively examined the ability of adult common marmosets (Callithrix jacchus), a highly vocal New World primate...

Reduced genetic diversity through inbreeding can negatively affect pathogen resistance. This relationship becomes more complicated in social species, such as social insects, since the chance of disease transmission increases with the frequency of interactions among individuals. However, social insects may benefit from social immunity, whereby individual physiological defenses may be bolstered by collective-level immune responses, such as grooming or sharing of antimicrobial substance through trophallaxis. We set out to determine whether differences in genetic diversity...

Additional file 4: Relationship between probability of identity (PID), probability of identity between siblings (PIDsib) and the number of genotyped SNP or microsatellite loci.

Captive breeding programs are often initiated to prevent species extinction until reintroduction into the wild can occur. However, the evolution of captive populations via inbreeding, drift, and selection can impair fitness, compromising reintroduction programs. To better understand the evolutionary response of species bred in captivity, we used nearly 5500 single nucleotide polymorphisms (SNPs) in populations of white-footed mice (Peromyscus leucopus) to measure the impact of breeding regimes on genomic diversity. We bred mice in captivity...

Insects feeding on plant sap, blood, and other nutritionally incomplete diets are typically associated with mutualistic bacteria that supplement missing nutrients. Herbivorous mammal dung contains more than 86% cellulose and lacks amino acids essential for insect development and reproduction. Yet one of the most ecologically necessary and evolutionarily successful groups of beetles, the dung beetles (Scarabaeinae) feeds primarily, or exclusively, on dung. These associations suggest that dung beetles may benefit from mutualistic bacteria that provide...

Background: Management requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon (Falco peregrinus) have been conducted, no similar studies have been done of the closely-related prairie falcon (F. mexicanus) and it is unclear how much genetic variation and population structure exists across the species’ range. Furthermore, the phylogenetic relationship of F. mexicanus relative to...

Juvenile striped bass reside in the Chesapeake Bay where they are likely to encounter hypoxia that could affect their metabolism and performance. The ecological success of this economically valuable species may depend on their ability to tolerate hypoxia and perform fitness-dependent activities in hypoxic waters. We tested whether there is a link between hypoxia tolerance (HT) and oxygen consumption rate (MO2) of juvenile striped bass measured while swimming in normoxic and hypoxic water, and to...

The smallest, fastest, repeated-use movements are propelled by power-dense elastic mechanisms, yet the key to their energetic control may be found in the latch-like mechanisms that mediate transformation from elastic potential energy to kinetic energy. Here we test how geometric latches enable consistent or variable outputs in ultrafast, spring-propelled systems. We constructed a reduced-order mathematical model of a spring-propelled system that uses a torque reversal (over-center) geometric latch. We parameterized the model to match the...

Background: Allegheny woodrats (Neotoma magister) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, Allegheny woodrat populations have experienced population declines throughout their range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of a small,...

Additional file 2: Summary statistics associated with nuclear genome sequencing, assembly and annotation.

Additional file 1: Microsatellite genotypes of woodrats sampled in 2009, 2011 and 2012 in the Palisades, NJ. The spreadsheets labeled “Raw Data” and “data GenAlEx” include the genotypes for twenty-eight individuals genotyped at 11 microsatellite loci. These individuals had relatively low genetic variability, as indicated by number of alleles (spreadsheets AFP and AGL), observed heterozygosity and expected heterozygosity (spreadsheet HFP).

Background: Life-history studies of wild bird populations often focus on the relationship between an individual’s condition and its capacity to mount an immune response, as measured by a commonly-employed assay of cutaneous immunity, the PHA skin test. In addition, haematocrit, the packed cell volume in relation to total blood volume, is often measured as an indicator of physiological performance. A multi-year study of a wild population of house wrens has recently revealed that those exhibiting...

1. Leaf defences vary widely among tree species, affecting rates of herbivory, survival and reproduction. 2. Two contrasting hypotheses account for variation in leaf defences among species. The first predicts that a slow life history, which is characteristic of larger seeded species adapted to resource-limited environments, is associated with well-defended leaves. The second, apparency theory, predicts that elevated leaf defences are necessitated for species that are more detectable to herbivores. 3. Here we use comparative...

Extinction events in the geological past are similar to the present-day biodiversity crisis in that they have a pronounced biogeography, producing dramatic changes in the spatial distributions of species. Reconstructing paleobiogeographic patterns from fossils therefore allows us to examine the long-term processes governing the formation of regional biotas, and potentially helps build spatially-explicit models for future biodiversity loss in a potential ‘6th mass extinction’ event. However, the extent to which biogeographic patterns can be preserved...

Multiple processes - including dispersal, morphological innovation, and habitat change - are frequently cited as catalysts for increased diversification. We investigate these processes and the causal linkages among them in the genus Cyphostemma (Vitaceae), a clade comprising ~200 species that is unique in the Vitaceae for its diversity of growth habits. We reconstruct time-calibrated evolutionary relationships among 64 species in the genus using five nuclear and chloroplast markers, and infer the group’s morphological and biogeographic...

Large and small mammalian herbivores are present in most vegetated areas in the Arctic, and often have large impacts on plant community composition and ecosystem functioning. The relative importance of different herbivores and especially how their specific impact on the vegetation varies across the Arctic is however poorly understood. Here, we investigate how large and small herbivores influence vegetation density and plant community composition in four arctic vegetation types in Scandinavia and Alaska. We used...

Habitat fragmentation and degradation have led to a proliferation of small and isolated populations that are vulnerable to genetic erosion. Reduction in habitat and concomitant declines in population connectivity can expediate the collapse of species that exist as natural metapopulations. In recent years, Allegheny woodrats (Neotoma magister) have experienced local extirpations and declines in genetic diversity across their range due to disease-related mortality, reduced food availability, and disruption of connectivity among subpopulations. In response, we...

Additional file 1: Microsatellite genotypes of woodrats sampled in 2009, 2011 and 2012 in the Palisades, NJ. The spreadsheets labeled “Raw Data” and “data GenAlEx” include the genotypes for twenty-eight individuals genotyped at 11 microsatellite loci. These individuals had relatively low genetic variability, as indicated by number of alleles (spreadsheets AFP and AGL), observed heterozygosity and expected heterozygosity (spreadsheet HFP).

Abstract Background Allegheny woodrats (Neotoma magister) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, the abundance of Allegheny woodrats has declined throughout the species’ range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of...