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Krojerová_Prokešová et al. 2018_genotypes
No full textFile with genotypes of all lynx individuals detected during the stud
Data from: Non-native insects dominate daytime pollination in a high-elevation Hawaiian dryland ecosystem
No full textPREMISE OF THE STUDY: Over one-third of the native flowering plant species in the Hawaiian Islands are listed as federally Threatened or Endangered. Lack of sufficient pollination could contribute to reductions in populations, reproduction, and genetic diversity among these species, but has been little studied.
METHODS: We used systematic observations and manual flower treatments to quantify flower visitation and outcrossing dependency of eight native (including four Endangered) plant species in a dryland ecosystem in Hawaii: Argemone glauca, Bidens menziesii, Dubautia linearis, Haplostachys haplostachya, Sida fallax, Silene lanceolata, Stenogyne angustifolia, Tetramolopium arenarium.
KEY RESULTS: During 576.36 hours of flower observations, only insects visited the flowers. Out of all recorded flower visits, 85% were performed by non-native species, particularly honeybee (Apis mellifera) and flies in the family Syrphidae. Some plant species received little visitation (e.g., S. angustifolia received one visit in 120 observation hours), while others were visited by a wide diversity of insects. The Endangered plant species were visited by fewer visitor taxa than were the common native plant species. For six of the focal plant species, bagging of flowers to exclude pollinators resulted in significant reductions in seed set.
CONCLUSIONS: The flower visitor community in this system, although heavily dominated by non-native insects, appears to be facilitating pollination for multiple plant species. Non-native insects may thus be sustaining biotic interactions otherwise threatened with disruption in this island ecosystem. This may be particularly important for the studied Endangered plant species, which exhibit fewer partners than the more common plant species.
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Raw data from flower visitation observations
No full textRaw data from flower visitation observations performed in a high-elevation dryland ecosystem on Hawaii Island from March 2015-May 2016
Data from: Improved inference of site-specific positive selection under a generalized parametric codon model when there are multinucleotide mutations and multiple nonsynonymous rates
No full textBackground: An excess of nonsynonymous substitutions, over neutrality, is considered evidence of positive Darwinian selection. Inference for proteins often relies on estimation of the nonsynonymous to synonymous ratio (ω=dN/dS) within a codon model. However, to ease computational difficulties, ω is typically estimated assuming an idealized substitution process where (i) all nonsynonymous substitutions have the same rate (regardless of impact on organism fitness) and (ii) instantaneous double and triple (DT) nucleotide mutations have zero probability (despite evidence that they can occur). It follows that estimates of ω represent an imperfect summary of the intensity of selection, and that tests based on the ω>1 threshold could be negatively impacted. Results: We developed a general-purpose parametric (GPP) modelling framework for codons. This novel approach allows specification of all possible instantaneous codon substitutions, including multiple nonsynonymous rates (MNRs) and instantaneous DT nucleotide changes. Existing codon models are specified as special cases of the GPP model. We use GPP models to implement likelihood ratio tests for ω>1 that accommodate MNRs and DT mutations. Through both simulation and real data analysis, we find that failure to model MNRs and DT mutations reduces power in some cases and inflates false positives in others. False positives under traditional M2a and M8 models were very sensitive to DT changes. This was exacerbated by the choice of frequency parameterization (GY vs. MG), with rates sometimes >90% under MG. By including MNRs and DT mutations, accuracy and power was greatly improved under the GPP framework. However, we also find that over-parameterized models can perform less well, and this can contribute to degraded performance of LRTs. Conclusions: We suggest GPP models should be used alongside traditional codon models. Further, all codon models should be deployed within an experimental design that includes (i) assessing robustness to model assumptions, and (ii) investigation of non-standard behaviour of MLEs. As the goal of every analysis is to avoid false conclusions, more work is needed on model selection methods that consider both the increase in fit engendered by a model parameter and the degree to which that parameter is affected by un-modelled evolutionary processes
Supplemental Figure 3
No full textSupplemental Figure 3: Representative histological figures from a mouse with graft versus host disease. GvHD inflammatory lesions in skin (A), lung (B), liver (C), kidney (D), pancreas (E), and sternum (F) are considered less severe, segmental to multifocal rather than more diffuse, and consist of more lymphocytes than histiocytes (insets) with fewer instances of granulomas compared to nivolumab treated BLT-NOG and BLT-NOG-EXL mice. Hematoxylin and eosin
Fig2
No full textUrea and albumin secretion from the standard (-KCs) and modified (+KCs) tissue model