pinecone/core-2020-05-10-deduplication huggingface dataset:
Age and quality-dependent DNA methylation correlate with melanin-based colouration in a wild bird

Secondary sexual trait expression can be influenced by fixed individual factors (such as genetic quality) but also by dynamic factors (such as age and environmentally induced gene expression) that may be associated with variation in condition or quality. In particular, melanin-based traits are known to relate to condition and there is a well-characterized genetic pathway underpinning their expression. However, the mechanisms linking variable trait expression to genetic quality remain unclear. One plausible mechanism is that genetic quality could influence trait expression via differential methylation and differential gene expression. We therefore conducted a pilot study examining DNA methylation at a candidate gene (agouti-related neuropeptide: AgRP) in the black grouse Lyrurus tetrix.  We specifically tested whether CpG methylation covaries with age and multilocus heterozygosity (a proxy of genetic quality) and from there whether the expression of a melanin-based ornament (UV blue chroma) correlates with DNA methylation.  Consistent with expectations, we found clear evidence for age- and heterozygosity-specific patterns of DNA methylation, with two CpG sites showing the greatest DNA methylation in highly heterozygous males at their peak age of reproduction. Furthermore, DNA methylation at three CpG sites was significantly positively correlated with UV blue chroma. Ours is the first study to our knowledge to document age- and quality-dependent variation in DNA methylation and to show that dynamic sexual trait expression across the lifespan of an organism is associated with patterns of DNA methylation.  Although we cannot demonstrate causality, our work provides empirical support for a mechanism that could potentially link key individual factors to variation in sexual trait expression in a wild vertebrate
Trophic transfer of biodiversity effects: functional equivalence of prey diversity and enrichment?

International audienceProducer diversity is frequently assumed to be detrimental to herbivores, because less edible taxa are more likely to dominate diverse communities. Many producers are, however, complementary in their resource use, and primary production is often positively related to producer diversity. We performed an experiment with microalgae and a generalist herbivore to explore the hypothesis that such positive effects are transferred up the food chain and are functionally comparable to effects of enrichment with a limiting resource. In both absence and presence of grazers, primary production was positively affected by both light supply and producer diversity. Survival, reproduction, and biomass of herbivores were also positively affected by light supply and producer diversity, with both factors contributing equally to grazer performance. We conclude that producer diversity can indeed have similar positive effects on secondary production as enrichment with a limiting resource and discuss conditions under which such positive effects are likely to dominate over negative ones
Where eagles soar : fine-resolution tracking reveals the spatiotemporal use of differential soaring modes in a large raptor

Unlike smaller raptors, which can readily use flapping flight, large raptors are mainly restricted to soaring flight due to energetic constraints. Soaring comprises of two main strategies: thermal and orographic soaring. These soaring strategies are driven by discrete uplift sources determined by the underlying topography and meteorological conditions in an area. High‐resolution GPS tracking of raptor flight allows the identification of these flight strategies and interpretation of the spatiotemporal occurrence of thermal and orographic soaring. In this study, we develop methods to identify soaring flight behaviors from high‐resolution GPS tracking data of Verreaux’s eagle Aquila verreauxii and analyze these data to understand the conditions that promote the use of thermal and orographic soaring. We use these findings to predict the use of soaring flight both spatially (across the landscape) and temporally (throughout the year) in two topographically contrasting regions in South Africa. We found that topography is important in determining the occurrence of soaring flight and that thermal soaring occurs in relatively flat areas which are likely to have good thermal uplift availability. The predicted use of orographic soaring was predominately determined by terrain slope. Contrary to our expectations, the topography and meteorology of eagle territories in the Sandveld promoted the use of soaring flight to a greater extent than in territories in the more mountainous Cederberg region. Spatiotemporal mapping of predicted flight behaviors can broaden our understanding of how large raptors like the Verreaux’s eagle use their habitat and how that links to energetics (as the preferential use of areas that maximize net energy gain is expected), reproductive success, and ultimately population dynamics. Understanding the fine‐scale landscape use and environmental drivers of raptor flight can also help to predict and mitigate potential detrimental effects of anthropogenic developments, such as mortality via collision with wind turbines.Publisher PDFPeer reviewe
Discovery of a multispecies shark aggregation and parturition area in the Ba Estuary, Fiji Islands

Population declines in shark species have been reported on local and global scales, with overfishing, habitat destruction and climate change posing severe threats. The\ud
 lack of species-specific baseline data on ecology and distribution of many sharks, however, makes conservation measures challenging. Here, we present a fisheries-independent shark survey from the Fiji Islands, where scientific knowledge on locally occurring elasmobranchs is largely still lacking despite the location’s role as a shark hotspot in the Pacific. Juvenile shark abundance in the fishing grounds of the Ba Estuary (north-western\ud
 Viti Levu) was assessed with a gillnet-and longline-based survey from December 2015 to April 2016. A total of 103 juvenile sharks identified as blacktip Carcharhinus limbatus (n = 57), scalloped hammerhead Sphyrna lewini\ud
 (n = 35), and great hammerhead Sphyrna mokarran (n = 11) sharks were captured, tagged, and released. The condition of umbilical scars (68% open or semihealed), mean sizes of individuals (±SD) (C. limbatus: 66.5 ± 3.8 cm, S. lewini: 51.8 ± 4.8 cm, S. mokarran 77.4 ± 2.8 cm), and the presence of these species over recent years (based on fishermen interviews), suggest that the Ba Estuary area is a critical habitat for multiple species that are classified as “Near Threatened” or “Endangered.”\ud
 Specifically, the area likely acts as a parturition ground over the studied period, and potentially as a subsequent nursery area. We identified subareas of high abundance and found that temperature, salinity and depth acted as small-scale environmental drivers of shark abundance. The data suggests a tendency for species-specific spatial use, both horizontally (i.e., between sampling areas) and vertically (i.e., across the\ud
 water column). These results enhance the understanding of shark ecology in Fiji and provide a scientific basis for the implementation of local conservation strategies that contribute to the protection of these threatened species
Permeability of the landscape matrix between amphibian breeding sites

For organisms that reproduce in discrete habitat patches, land cover between patches (known as the matrix) is important for dispersal among breeding sites. Models of patchy populations often incorporate information on the permeability of the matrix to dispersal, sometimes based on expert opinion. I estimated the relative resistance to gene flow of land cover types and barriers using FST calculated from microsatellite markers in two amphibians, within an 800 km2 area in northern Switzerland. The species included a frog (Rana temporaria: 996 individuals, 48 populations, 7 markers) and a newt (Triturus alpestris: 816 individuals, 41 populations, 7 markers). Open fields and urban areas were more resistant to gene flow than forested land; roads and highways also reduced permeability. Results were similar for the two species. However, differences in resistance among matrix elements were relatively low: gene flow through urban areas was reduced by only 24-42% relative to forest; a divided highway reduced gene flow by 11-40% and was 7-8 times more resistant than a secondary road. These data offer an empirically-based alternative to expert opinion for setting relative resistance values in landscape models
Human-induced marine ecological degradation: micropaleontological perspectives

We analyzed published downcore microfossil records from 150 studies and reinterpreted them from an ecological degradation perspective to address the following critical but still imperfectly answered questions: (1) How is the timing of human-induced degradation of marine ecosystems different among regions? (2) What are the dominant causes of human-induced marine ecological degradation? (3) How can we better document natural variability and thereby avoid the problem of shifting baselines of comparison as degradation progresses over time? The results indicated that: (1) ecological degradation in marine systems began significantly earlier in Europe and North America ( approximately 1800s) compared with Asia (post-1900) due to earlier industrialization in European and North American countries, (2) ecological degradation accelerated globally in the late 20th century due to post-World War II economic growth, (3) recovery from the degraded state in late 20th century following various restoration efforts and environmental regulations occurred only in limited localities. Although complex in detail, typical signs of ecological degradation were diversity decline, dramatic changes in total abundance, decrease in benthic and/or sensitive species, and increase in planktic, resistant, toxic, and/or introduced species. The predominant cause of degradation detected in these microfossil records was nutrient enrichment and the resulting symptoms of eutrophication, including hypoxia. Other causes also played considerable roles in some areas, including severe metal pollution around mining sites, water acidification by acidic wastewater, and salinity changes from construction of causeways, dikes, and channels, deforestation, and land clearance. Microfossils enable reconstruction of the ecological history of the past 10(2)-10(3) years or even more, and, in conjunction with statistical modeling approaches using independent proxy records of climate and human-induced environmental changes, future research will enable workers to better address Shifting Baseline Syndrome and separate anthropogenic impacts from background natural variability.published_or_final_versio
Latitudinal effects on crown shape evolution

Large variations in crown shape are observed across the globe, from plants with wide and deep crowns to those with leaves clustered at the top. While there have been advances in the large‐scale monitoring of forests, little is known about factors driving variations in crown shape with environmental conditions. Previous theoretical research suggests a gradient in crown shape with latitude, due to the effects of sun angle. Yet, it remains unclear whether such changes are also predicted under competition. Using a size‐structured forest‐growth model that incorporates self‐shading from plants and competitive shading from their neighbors, we investigate how changes in site productivity and sun angle shape crown evolution. We consider evolution in two traits describing the top‐heaviness and width‐to‐height ratio of crowns, shaped by trade‐offs reflecting the costs and benefits of alternative architectures. In top‐heavy trees, most of the leaves are at the top half of the trunk. We show that, contrary to common belief, the angle of sun beams per se has only a weak influence on crown shapes, except at low site productivity. By contrast, reduced site productivity has a strong effect, with trees growing in less productive sites keeping their leaves closer to the ground. The crown width‐to‐height ratio is generally higher at a lower site productivity, but this trait is not strongly influenced by any environmental factor. This theoretical analysis brings into question established beliefs about the effects of latitude on crown shapes. By introducing geometry‐related growth constraints caused by shading from both the surrounding forest and the tree on itself, and costs for constructing and maintaining a three‐dimensional crown, our analysis suggests crown shapes may vary with latitude, mostly via effects on overall site productivity, and less because of the angle of the sun
Color vision models : some simulations, a general n-dimensional model, and the colourvision R package

The development of color vision models has allowed the appraisal of color vision independent
of the human experience. These models are now widely used in ecology
and evolution studies. However, in common scenarios of color measurement, color
vision models may generate spurious results. Here I present a guide to color vision
modeling (Chittka (1992, Journal of Comparative Physiology A, 170, 545) color hexagon,
Endler & Mielke (2005, Journal Of The Linnean Society, 86, 405) model, and the
linear and log-linear
receptor noise limited models (Vorobyev & Osorio 1998,
Proceedings of the Royal Society B, 265, 351; Vorobyev et al. 1998, Journal of
Comparative Physiology A, 183, 621)) using a series of simulations, present a unified
framework that extends and generalize current models, and provide an R package to
facilitate the use of color vision models. When the specific requirements of each
model are met, between-model
results are qualitatively and quantitatively similar.
However, under many common scenarios of color measurements, models may generate
spurious values. For instance, models that log-transform
data and use relative
photoreceptor outputs are prone to generate spurious outputs when the stimulus
photon catch is smaller than the background photon catch; and models may generate
unrealistic predictions when the background is chromatic (e.g. leaf reflectance) and
the stimulus is an achromatic low reflectance spectrum. Nonetheless, despite differences,
all three models are founded on a similar set of assumptions. Based on that, I
provide a new formulation that accommodates and extends models to any number of
photoreceptor types, offers flexibility to build user-defined
models, and allows users
to easily adjust chromaticity diagram sizes to account for changes when using different
number of photoreceptors
Quantifying dispersal between marine protected areas by a highly mobile species, the bottlenose dolphin, Tursiops truncatus

M.N. was funded by a Crawford‐Hayes studentship and National Parks and Wildlife Service (NPWS), Department of Culture, Heritage and Gaeltacht, Ireland. E.D. was supported by the Beaufort Marine Research Award in Fish Population Genetics funded by the Irish Government under the Sea Change Programme. Financial support for A.D.F. was provided by the Welsh Government and Higher Education Funding Council for Wales through the Sêr Cymru National Research Network for Low Carbon, Energy and Environment, and from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska‐Curie grant agreement No. 663830.The functioning of marine protected areas (MPAs) designated for marine megafauna has been criticized due to the high mobility and dispersal potential of these taxa. However, dispersal within a network of small MPAs can be beneficial as connectivity can result in increased effective population size, maintain genetic diversity, and increase robustness to ecological and environmental changes making populations less susceptible to stochastic genetic and demographic effects (i.e., Allee effect). Here, we use both genetic and photo-identification methods to quantify gene flow and demographic dispersal between MPAs of a highly mobile marine mammal, the bottlenose dolphin Tursiops truncatus. We identify three populations in the waters of western Ireland, two of which have largely nonoverlapping core coastal home ranges and are each strongly spatially associated with specific MPAs. We find high site fidelity of individuals within each of these two coastal populations to their respective MPA. We also find low levels of demographic dispersal between the populations, but it remains unclear whether any new gametes are exchanged between populations through these migrants (genetic dispersal). The population sampled in the Shannon Estuary has a low estimated effective population size and appears to be genetically isolated. The second coastal population, sampled outside of the Shannon, may be demographically and genetically connected to other coastal subpopulations around the coastal waters of the UK. We therefore recommend that the methods applied here should be used on a broader geographically sampled dataset to better assess this connectivity.Publisher PDFPeer reviewe
Phosphogenesis in the 2460 and 2728 million-year-old banded iron formations as evidence for biological cycling of phosphate in the early biosphere

The banded iron formation deposited during the first 2 billion years of Earth's history holds the key to understanding the interplay between the geosphere and the early biosphere at large geological timescales. The earliest ore-scale phosphorite depositions formed almost at approximately 2.0-2.2 billion years ago bear evidence for the earliest bloom of aerobic life. The cycling of nutrient phosphorus and how it constrained primary productivity in the anaerobic world of Archean-Palaeoproterozoic eons are still open questions. The controversy centers about whether the precipitation of ultrafine ferric oxyhydroxide due to the microbial Fe(II) oxidation in oceans earlier than 1.9 billion years substantially sequestrated phosphate, and whether this process significantly limited the primary productivity of the early biosphere. In this study, we report apatite radial flowers of a few micrometers in the 2728 million-year-old Abitibi banded iron formation and the 2460 million-year-old Kuruman banded iron formation and their similarities to those in the 535 million-year-old Lower Cambrian phosphorite. The lithology of the 535 Million-year-old phosphorite as a biosignature bears abundant biomarkers that reveal the possible similar biogeochemical cycling of phosphorus in the Later Archean and Palaeoproterozoic oceans. These apatite radial flowers represent the primary precipitation of phosphate derived from the phytoplankton blooms in the euphotic zones of Neoarchean and Palaoeproterozoic oceans. The unbiased distributions of the apatite radial flowers within sub-millimeter bands do not support the idea of an Archean Crisis of Phosphate. This is the first report of the microbial mediated mineralization of phosphorus before the Great Oxidation Event when the whole biosphere was still dominated by anaerobic microorganisms.published_or_final_versio
Host diet mediates a negative relationship between abundance and diversity of <i>Drosophila</i> gut microbiota.

Nutrient supply to ecosystems has major effects on ecological diversity, but it is unclear to what degree the shape of this relationship is general versus dependent on the specific environment or community. Although the diet composition in terms of the source or proportions of different nutrient types is known to affect gut microbiota composition, the relationship between the quantity of nutrients supplied and the abundance and diversity of the intestinal microbial community remains to be elucidated. Here, we address this relationship using replicate populations of  &lt;i&gt;Drosophila melanogaster&lt;/i&gt;  maintained over multiple generations on three diets differing in the concentration of yeast (the only source of most nutrients). While a 6.5-fold increase in yeast concentration led to a 100-fold increase in the total abundance of gut microbes, it caused a major decrease in their alpha diversity (by 45-60% depending on the diversity measure). This was accompanied by only minor shifts in the taxonomic affiliation of the most common operational taxonomic units (OTUs). Thus, nutrient concentration in host diet mediates a strong negative relationship between the nutrient abundance and microbial diversity in the  &lt;i&gt;Drosophila&lt;/i&gt;  gut ecosystem
Are Ponto-Caspian species able to cross salinity barriers? A case study of the gammarid Pontogammarus maeoticus

Recently, Ponto-Caspian species (i.e., area of Azov, Black, and Caspian Seas) have invaded brackish and freshwater habitats of the North and Baltic Seas and the Laurentian Great Lakes in much higher numbers than expected based on shipping frequency and environmental conditions among these regions. Therefore, it has been suggested that Ponto-Caspian species may have inherent advantages over other species in colonizing new habitats, or that they are of freshwater origin. Artificial selection offers the possibility to investigate phenotypic plasticity, shifts in environmental tolerance, and heritability of environmentally sensitive traits; therefore, in this study, we conducted artificial selection experiments on Ponto-Caspian amphipod Pontogammarus maeoticus collected from 10 PSU to evaluate adaptation capacity of this species to different salinities, and to shed additional light on a possible freshwater origin of Ponto-Caspian invaders. Our results indicated that selection to lower salinity than that of the population's ambient salinity is possible within few generations due to a likely existence of standing polymorphic variation for selection to act on. In contrast, selection to higher salinity was unsuccessful because the phenotypic variation was mainly caused by environmental variance and therefore might depend on new mutations. Consequently, the results of our study suggest that the tested species might be of freshwater origin and lacks necessary genetic background for adaptation to fully marine conditions. Further selection studies using more species and populations, as well as molecular techniques, should be conducted to elucidate if other Ponto-Caspian invaders are of freshwater origin as well