Genomics meets applied ecology: Characterizing habitat quality for sloths in a tropical agroecosystem

Understanding how habitat quality in heterogeneous landscapes governs the distribution and fitness of individuals is a fundamental aspect of ecology. While mean individual fitness is generally considered a key to assessing habitat quality, a comprehensive understanding of habitat quality in heterogeneous landscapes requires estimates of dispersal rates among habitat types. The increasing accessibility of genomic approaches, combined with field‐based demographic methods, provides novel opportunities for incorporating dispersal estimation into assessments of habitat quality. In this study, we integrated genomic kinship approaches with field‐based estimates of fitness components and approximate Bayesian computation (ABC) procedures to estimate habitat‐specific dispersal rates and characterize habitat quality in two‐toed sloths (Choloepus hoffmanni) occurring in a Costa Rican agricultural ecosystem. Field‐based observations indicated that birth and survival rates were similar in a sparsely shaded cacao farm and adjacent cattle pasture–forest mosaic. Sloth density was threefold higher in pasture compared with cacao, whereas home range size and overlap were greater in cacao compared with pasture. Dispersal rates were similar between the two habitats, as estimated using ABC procedures applied to the spatial distribution of pairs of related individuals identified using 3,431 single nucleotide polymorphism and 11 microsatellite locus genotypes. Our results indicate that crops produced under a sparse overstorey can, in some cases, constitute lower‐quality habitat than pasture–forest mosaics for sloths, perhaps because of differences in food resources or predator communities. Finally, our study demonstrates that integrating field‐based demographic approaches with genomic methods can provide a powerful means for characterizing habitat quality for animal populations occurring in heterogeneous landscapes.     

Genetic and morphological evidence of a geographically widespread hybrid zone between two crocodile species,Crocodylus acutus and Crocodylus moreletii

Hybrid zones represent natural laboratories to study gene flow, divergence and the nature of species boundaries between closely related taxa. We evaluated the level and extent of hybridization between Crocodylus moreletii and Crocodylus acutus using genetic and morphological data on 300 crocodiles from 65 localities. To our knowledge, this is the first genetic study that includes the entire historic range and sympatric zone of the two species. Contrary to expectations, Bayesian admixture proportions and maximum‐likelihood estimates of hybrid indexes revealed that most sampled crocodiles were admixed and that the hybrid zone is geographically extensive, extending well beyond their historical region of sympatry. We identified a few geographically isolated, nonadmixed populations of both parental species. Hybrids do not appear to be F₁s or recent backcrosses, but rather are more likely later‐generation hybrids, suggesting that hybridization has been going on for several to many generations and is mostly the result of natural processes. Crocodylus moreletii is not the sister species of C. acutus, suggesting that the hybrid zone formed from secondary contact rather than primary divergence. Nonadmixed individuals from the two species were distinguishable based on morphological characters, whereas hybrids had a complex mosaic of morphological characters that hinders identification in the wild. Very few nonadmixed C. acutus and C. moreletii populations exist in the wild. Consequently, the last nonadmixed C. moreletii populations have become critically endangered. Indeed, not only the parental species but also the naturally occurring hybrids should be considered for their potential conservation value.     

Phenological change in a spring ephemeral: implications for pollination and plant reproduction

Climate change has had numerous ecological effects, including species range shifts and altered phenology. Altering flowering phenology often affects plant reproduction, but the mechanisms behind these changes are not well‐understood. To investigate why altering flowering phenology affects plant reproduction, we manipulated flowering phenology of the spring herb Claytonia lanceolata (Portulacaceae) using two methods: in 2011–2013 by altering snow pack (snow‐removal vs. control treatments), and in 2013 by inducing flowering in a greenhouse before placing plants in experimental outdoor arrays (early, control, and late treatments). We measured flowering phenology, pollinator visitation, plant reproduction (fruit and seed set), and pollen limitation. Flowering occurred approx. 10 days earlier in snow‐removal than control plots during all years of snow manipulation. Pollinator visitation patterns and strength of pollen limitation varied with snow treatments, and among years. Plants in the snow removal treatment were more likely to experience frost damage, and frost‐damaged plants suffered low reproduction despite lack of pollen limitation. Plants in the snow removal treatment that escaped frost damage had higher pollinator visitation rates and reproduction than controls. The results of the array experiment supported the results of the snow manipulations. Plants in the early and late treatments suffered very low reproduction due either to severe frost damage (early treatment) or low pollinator visitation (late treatment) relative to control plants. Thus, plants face tradeoffs with advanced flowering time. While early‐flowering plants can reap the benefits of enhanced pollination services, they do so at the cost of increased susceptibility to frost damage that can overwhelm any benefit of flowering early. In contrast, delayed flowering results in dramatic reductions in plant reproduction through reduced pollination. Our results suggest that climate change may constrain the success of early‐flowering plants not through plant‐pollinator mismatch but through the direct impacts of extreme environmental conditions.     

Behavioral mechanisms leading to improved fitness in a subsidized predator

General mechanisms underlying the distribution and fitness of synanthropic predators in human-influenced landscapes remain unclear. Under the consumer resource-matching hypothesis, synanthropes are expected to distribute themselves among habitats according to resource availability, such that densities are greater in human-subsidized habitats, but mean individual fitness is equal among habitats because of negative density dependence. However, “under-matching” to human food resources can occur, because dominant individuals exclude subordinates from subsidized habitats and realize relatively high fitness. We integrated physiological, behavioral, and demographic information to test resource-matching hypotheses in Steller’s jays (Cyanocitta stelleri), a synanthropic nest predator, to understand how behavior and social systems can influence how synanthropes respond to food subsidies. Jays consumed more human foods at subsidized (park campground) sites than jays at unsubsidized (interior forest) sites based on stable isotope analyses. Jays that occurred at higher densities were in better body condition (based on feather growth bars and lipid analyses), and had greater reproductive output at subsidized than unsubsidized sites. Jays with breeding territories in subsidized sites maintained relatively small home ranges that overlapped with multiple conspecifics, and exhibited a social system where dominant individuals typically won contests over food. Thus, jays appeared to be under-matched to prevalent resource subsidies despite high densities and behaviors expected to lead to resource matching. Our results also indicate that local resource subsidies within protected areas can result in source habitats for synanthropes, potentially impacting sensitive species over broader spatial scales.     

In Situ,Fast, High‐Temperature Synthesis of Nickel Nanoparticles in Reduced Graphene Oxide Matrix

For the first time, a fast heating–cooling process is reported for the synthesis of carbon‐coated nickel (Ni) nanoparticles on a reduced graphene oxide (RGO) matrix (nano‐Ni@C/RGO) as a high‐performance H₂O₂ fuel catalyst. The Joule heating temperature can reach up to ≈2400 K and the heating time can be less than 0.1 s. Ni microparticles with an average diameter of 2 µm can be directly converted into nanoparticles with an average diameter of 75 nm. The Ni nanoparticles embedded in RGO are evaluated for electro‐oxidation performance as a H₂O₂ fuel in a direct peroxide–peroxide fuel cell, which exhibits an electro‐oxidation current density of 602 mA cm^?2 at 0.2 V (vs Ag/AgCl), ≈150 times higher than the original Ni microparticles embedded in the RGO matrix (micro‐Ni/RGO). The high‐temperature, fast Joule heating process also leads to a 4–5 nm conformal carbon coating on the surface of the Ni nanoparticles, which anchors them to the RGO nanosheets and leads to an excellent catalytic stability. The newly developed nano‐Ni@C/RGO composites by Joule heating hold great promise for a range of emerging energy applications, including the advanced anode materials of fuel cells.     

Quantitative characterization of virus-like particles by asymmetrical flow field flow fractionation, electrospray differential mobility analysis, and transmission electron microscopy

Here we characterize virus-like particles (VLPs) by three very distinct, orthogonal, and quantitative techniques: electrospray differential mobility analysis (ES-DMA), asymmetric flow field-flow fractionation with multi-angle light scattering detection (AFFFF-MALS) and transmission electron microscopy (TEM). VLPs are biomolecular particles assembled from viral proteins with applications ranging from synthetic vaccines to vectors for delivery of gene and drug therapies. VLPs may have polydispersed, multimodal size distributions, where the size distribution can be altered by subtle changes in the production process. These three techniques detect subtle size differences in VLPs derived from the non-enveloped murine polyomavirus (MPV) following: (i) functionalization of the surface of VLPs with an influenza viral peptide fragment; (ii) packaging of foreign protein internally within the VLPs; and (iii) packaging of genomic DNA internally within the VLPs. These results demonstrate that ES-DMA and AFFFF-MALS are able to quantitatively determine VLP size distributions with greater rapidity and statistical significance than TEM, providing useful technologies for product development and process analytics.     

Soliton/exciton transport in proteins

The study of electron/proton transport in alpha-helix sections of proteins have illustrated the existence of soliton-like mechanisms. Recently, Ciblis and Cosic extended investigation to the existence of possible like soliton-type mechanisms in other parts of the protein. They used Quantum Hamiltonian analysis to investigate. In this paper, we investigate the same problem but we use Classical Hamiltonian analysis in our investigation.     

Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants

Detailed information about the geographic distribution of genetic and genomic variation is necessary to better understand the organization and structure of biological diversity. In particular, spatial isolation within species and hybridization between them can blur species boundaries and create evolutionary relationships that are inconsistent with a strictly bifurcating tree model. Here, we analyse genome‐wide DNA sequence and genetic ancestry variation in Lycaeides butterflies to quantify the effects of admixture and spatial isolation on how biological diversity is organized in this group. We document geographically widespread and pervasive historical admixture, with more restricted recent hybridization. This includes evidence supporting previously known and unknown instances of admixture. The genome composition of admixed individuals varies much more among than within populations, and tree‐ and genetic ancestry‐based analyses indicate that multiple distinct admixed lineages or populations exist. We find that most genetic variants in Lycaeides are rare (minor allele frequency <0.5%). Because the spatial and taxonomic distributions of alleles reflect demographic and selective processes since mutation, rare alleles, which are presumably younger than common alleles, were spatially and taxonomically restricted compared with common variants. Thus, we show patterns of genetic variation in this group are multifaceted, and we argue that this complexity challenges simplistic notions concerning the organization of biological diversity into discrete, easily delineated and hierarchically structured entities.     

Experimental evidence for ecological selection on genome variation in the wild

Understanding natural selection's effect on genetic variation is a major goal in biology, but the genome‐scale consequences of contemporary selection are not well known. In a release and recapture field experiment we transplanted stick insects to native and novel host plants and directly measured allele frequency changes within a generation at 186 576 genetic loci. We observed substantial, genome‐wide allele frequency changes during the experiment, most of which could be attributed to random mortality (genetic drift). However, we also documented that selection affected multiple genetic loci distributed across the genome, particularly in transplants to the novel host. Host‐associated selection affecting the genome acted on both a known colour‐pattern trait as well as other (unmeasured) phenotypes. We also found evidence that selection associated with elevation affected genome variation, although our experiment was not designed to test this. Our results illustrate how genomic data can identify previously underappreciated ecological sources and phenotypic targets of selection.