skip to main content


Search for: All records

Creators/Authors contains: "Nielsen, Rasmus"

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. Abstract

    Aposematic organisms rely on their conspicuous appearance to signal that they are defended and unpalatable. Such phenotypes are strongly tied to survival and reproduction. Aposematic colors and patterns are highly variable; however, the genetic, biochemical, and physiological mechanisms producing this conspicuous coloration remain largely unidentified. Here, we identify genes potentially affecting color variation in two color morphs of Ranitomeya imitator: the orange-banded Sauce and the redheaded Varadero morphs. We examine gene expression in black and orange skin patches from the Sauce morph and black and red skin patches from the Varadero morph. We identified genes differentially expressed between skin patches, including those that are involved in melanin synthesis (e.g. mlana, pmel, tyrp1), iridophore development (e.g. paics, ppat, ak1), pteridine synthesis (e.g. gch1, pax3-a, xdh), and carotenoid metabolism (e.g. dgat2, rbp1, scarb2). In addition, using weighted correlation network analysis, we identified the top 50 genes with high connectivity from the most significant network associated with gene expression differences between color morphs. Of these 50 genes, 13 were known to be related to color production (gch1, gmps, gpr143, impdh1, mc1r, pax3-a, pax7, ppat, rab27a, rlbp1, tfec, trpm1, xdh).

     
    more » « less
  2. Abstract

    Skin coloration and patterning play a key role in animal survival and reproduction. As a result, color phenotypes have generated intense research interest. In aposematic species, color phenotypes can be important in avoiding predation and in mate choice. However, we still know little about the underlying genetic mechanisms of color production, particularly outside of a few model organisms. Here we seek to understand the genetic mechanisms underlying the production of different colors and how these undergo shifting expression patterns throughout development. To answer this, we examine gene expression of two different color patches(yellow and green) in a developmental time series from young tadpoles through adults in the poison frogOophaga pumilio.We identified six genes that were differentially expressed between color patches in every developmental stage (casq1, hand2, myh8, prva, tbx3,andzic1).Of these,hand2, myh8, tbx3,andzic1have either been identified or implicated as important in coloration in other taxa.Casq1andprvabuffer Ca2+and are a Ca2+transporter, respectively, and may play a role in preventing autotoxicity to pumiliotoxins, which inhibit Ca2+-ATPase activity. We identify further candidate genes (e.g.,adh, aldh1a2, asip, lef1, mc1r, tyr, tyrp1, xdh), and identify a suite of hub genes that likely play a key role in integumental reorganization during development (e.g., collagen type I–IV genes, lysyl oxidases) which may also affect coloration via structural organization of chromatophores that contribute to color and pattern. Overall, we identify the putative role of a suite of candidate genes in the production of different color types in a polytypic, aposematic species.

     
    more » « less
  3. Abstract

    A common goal in evolutionary biology is to discern the mechanisms that produce the astounding diversity of morphologies seen across the tree of life. Aposematic species, those with a conspicuous phenotype coupled with some form of defence, are excellent models to understand the link between vivid colour pattern variations, the natural selection shaping it, and the underlying genetic mechanisms underpinning this variation. Mimicry systems in which species share a conspicuous phenotype can provide an even better model for understanding the mechanisms of colour production in aposematic species, especially if comimics have divergent evolutionary histories. Here we investigate the genetic mechanisms by which mimicry is produced in poison frogs. We assembled a 6.02‐Gbp genome with a contig N50 of 310 Kbp, a scaffold N50 of 390 Kbp and 85% of expected tetrapod genes. We leveraged this genome to conduct gene expression analyses throughout development of four colour morphs ofRanitomeya imitatorand two colour morphs from bothR. fantasticaandR. variabiliswhichR. imitatormimics. We identified a large number of pigmentation and patterning genes differentially expressed throughout development, many of them related to melanophores/melanin, iridophore development and guanine synthesis. We also identify the pteridine synthesis pathway (including genes such asqdprandxdh) as a key driver of the variation in colour between morphs of these species, and identify several plausible candidates for colouration in vertebrates (e.g.cd36,ep‐cadherinandperlwapin). Finally, we hypothesise that keratin genes (e.g.krt8) are important for producing different structural colours within these frogs.

     
    more » « less
  4. Abstract Background

    Inference of person-to-person transmission networks using surveillance data is increasingly used to estimate spatiotemporal patterns of pathogen transmission. Several data types can be used to inform transmission network inferences, yet the sensitivity of those inferences to different data types is not routinely evaluated.

    Methods

    The influence of different combinations of spatial, temporal, and travel-history data on transmission network inferences forPlasmodium falciparummalaria were evaluated.

    Results

    The information content of these data types may be limited for inferring person-to-person transmission networks and may lead to an overestimate of transmission. Only when outbreaks were temporally focal or travel histories were accurate was the algorithm able to accurately estimate the reproduction number under control,Rc. Applying this approach to data from Eswatini indicated that inferences ofRcand spatiotemporal patterns therein depend upon the choice of data types and assumptions about travel-history data.

    Conclusions

    These results suggest that transmission network inferences made with routine malaria surveillance data should be interpreted with caution.

     
    more » « less
  5. The abundance of media options is a central feature of today’s information environment. Many accounts, often based on analysis of desktop-only news use, suggest that this increased choice leads to audience fragmentation, ideological segregation, and echo chambers with no cross-cutting exposure. Contrary to many of those claims, this paper uses observational multiplatform data capturing both desktop and mobile use to demonstrate that coexposure to diverse news is on the rise, and that ideological self-selection does not explain most of that coexposure. We show that mainstream media outlets offer the common ground where ideologically diverse audiences converge online, though our analysis also reveals that more than half of the US online population consumes no online news, underlining the risk of increased information inequality driven by self-selection along lines of interest. For this study, we use an unprecedented combination of observed data from the United States comprising a 5-y time window and involving tens of thousands of panelists. Our dataset traces news consumption across different devices and unveils important differences in news diets when multiplatform or desktop-only access is used. We discuss the implications of our findings for how we think about the current communication environment, exposure to news, and ongoing attempts to limit the effects of misinformation. 
    more » « less
  6. Buerkle, Alex (Ed.)
  7. Parsch, John (Ed.)
    Abstract Genetic introgression not only provides material for adaptive evolution but also confounds our understanding of evolutionary history. This is particularly true for canids, a species complex in which genome sequencing and analysis has revealed a complex history of admixture and introgression. Here, we sequence 19 new whole genomes from high-altitude Tibetan and Himalayan wolves and dogs and combine these into a larger data set of 166 whole canid genomes. Using these data, we explore the evolutionary history and adaptation of these and other canid lineages. We find that Tibetan and Himalayan wolves are closely related to each other, and that ∼39% of their nuclear genome is derived from an as-yet-unrecognized wolf-like lineage that is deeply diverged from living Holarctic wolves and dogs. The EPAS1 haplotype, which is present at high frequencies in Tibetan dog breeds and wolves and confers an adaptive advantage to animals living at high altitudes, was probably derived from this ancient lineage. Our study underscores the complexity of canid evolution and demonstrates how admixture and introgression can shape the evolutionary trajectories of species. 
    more » « less
  8. The cold, wet climate of the Arctic has led to the extraordinary preservation of archaeological sites and materials that offer important contributions to the understanding of our common cultural and ecological history. This potential, however, is quickly disappearing due to climate-related variables, including the intensification of permafrost thaw and coastal erosion, which are damaging and destroying a wide range of cultural and environmental archives around the Arctic. In providing an overview of the most important effects of climate change in this region and on archaeological sites, the authors propose the next generation of research and response strategies, and suggest how to capitalise on existing successful connections among research communities and between researchers and the public. 
    more » « less