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Work Journal 2019

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Work Journal 2019 January Monday, January 1 I rose early this morning and worked on cleaning up my late 2018 work journal, working for an hour on this. Wednesday, January 3 We stopped by work this afternoon so that I could pick up my most recent SF50 and other documentation requisite for my unemployment application. I had received a box containing 199 Archaeognatha specimens in 88 vials. Monday, January 28 To do: Time sheet AKES meeting arrangements. Associate travel card with Concur account. Refuge Notebook catch-up Biology News entries, new literature to add to Bio publications bibliography page. Biota of Canada post to akentsoc.org Finish late 2018 work journal. Look over bristletails received. I worked on adding images and scripts to my 2018 work journal, trying to finalize it. John asked me to post the recent Refuge Notebook articles from December, so I formatted and posted these. I also made posts to Biology News. Tuesday, January 29 To do: AKES meeting arrangements. STDP Final Report to Liz Figure out AKES meeting topic and get going on presentation. Restart AWCC slurm job that was canceled on 26.Dec.2018. Take care of vehicle. New literature to add to Bio publications bibliography page and to our literature database. Biota of Canada post to akentsoc.org Finish late 2018 work journal. Arrange for return shipping of Betula specimens. Look over bristletails received. Debbie helped me make travel arrangements for Fairbanks, so this is a go. Now I need to figure out my talk since I was not able to work on the alpine defoliation project in January as I had intended. Liz Graham wrote, asking that I fill in the STDP report review. I started looking through that dataset for notable records. Pissodes fiskei is not in our Alaska checklist. I checked that sequence again. It is closest to a sequence of Pissodes costatus, which we have in Alaska. There were no other new records. I need to get this into a publication of some sort. I also need to start an Alaska library on github. I worked on re-submitting AWCC/Caribou Hills data for the ITSx step (see script). Examining specimen with barcode label UAM100185885 (KNWR:Ento:11301), from Bay View Cemetery. This is female Petrobiinae, with sole shaped lateral ocelli. There appear to be 2+2 eversible vesicles on segment VI, but it is a little hard to tell because only the outer pair are ever eversed. This looks like Pedetontus s. str. KNWR:Ento:11301, label. KNWR:Ento:11301, face. Wednesday, January 30 To do: Figure out AKES meeting topic and get going on presentation. New literature to add to Bio publications bibliography page and to our literature database. Biota of Canada post to akentsoc.org Finish late 2018 work journal. Arrange for return shipping of Betula specimens. Look over bristletails received. I sorted the remaining 67 or so vials of bristletail specimens given to me by Rod Crawford, not opening the vials, but just roughly sorting them based on what they appeared to be. There appear to be less than 88 vials listed on the loan, but this is ok. I was hoping to see some Petridiobius specimens, but there were none. There was more Pedetontus s. str. than anything, followed by Pedetontus cf. submutans and Machilinus. Most of these specimens had been sifted from moss or litter. Sorted vials of bristletails from Rod Crawford. I finished adding material to my late 2018 work journal including scans, references, etc. Needing to figure out what to present on next week at the AKES meeting, I resumed the AKES Newsletter article on soil fungi affected by earthworms at Stormy Lake with the intention of adding affects to soil fungi to the earthworm presentation I gave in the fall. See the R script. Biplot of a PCA of Stormy Lake soil fungi occurrence data. Note that all nightcrawler- infested sites (1-3) are to the left of the nightcrawler-free sites (4-6). Frequencies of occurrence of soil fungal OTUs. Thursday, January 31 To do: Pay Arctos invoices. Work up Stormy Lake soil fungi data for AKES Newsletter and presentation. New literature to add to Bio publications bibliography page and to our literature database. Biota of Canada post to akentsoc.org Arrange for return shipping of Betula specimens. I paid the Arctos invoices. I helped Todd with tagging eight sea otters pelts. Before the winter is over I want to ski down to the trail intersection near Slikok Lake where I collected specimen MOBIL6660-18 last year. This was a Diptera larva collected from a spring in winter. There is no close match for the COI sequence obtained from this specimen on BOLD; the closest match is 89.92% similarity and is identified as Diptera. Other matches over 89% are Chironomidae. I would like to collect more specimens to try to put a genus name on these using morphology. Chironomid larva specimen MOBIL6660-18. I requested that records from dataset DS-BOWSER be included the next time that the BOLD BIN algorithm (Ratnasingham et al., 2013) is run. This has not been done for some time. For example, the chironomid specimen referred to above collected in March 2018 has not yet been assigned to a BIN despite having a clean, full-length sequence. I did look at results of the PIPITS analysis of 2017 Stormy Lake fungal data (see script). I also skied down the spring where I had collected that mystery chironomid before and collected more sediment, both from the spring and from the stream where it crosses the snowmachine trail. Sediment sample taken from spring. Sediment sample taken from stream below spring where it crosses the trail. February Friday, February 1 To do: Post this week's Refuge Notebook article. Look at samples collected yesterday. Work up Stormy Lake soil fungi data for AKES Newsletter and presentation. New literature to add to Bio publications bibliography page and to our literature database. Biota of Canada post to akentsoc.org Arrange for return shipping of Betula specimens. I looked through the sediment sample from the stream collected yesterday. There were many ostracods, a few tiny worms, two caddisfly larvae, and three Diptera larvae, each different from the other. I posted this week's Refuge Notebook article, starting a new volume for the year. I updated the KNWR Biology's publications bibliography and posted new literature announcements to http://www.akentsoc.org/. I resumed work on the Stormy Lake fungal data (see script). I am excited to have just learned about FUNGuild (Nguyen et al., 2016). After some formatting fixes (removing spaces, etc.) I was able to submit my OTU table to FUNGuild at http://www.stbates.org/guilds/app.php. Guilds v1.0 Beta report: - 386 assignments were made on OTUs within the input file! - Total calculating time = 8.8 seconds! I looked through these results in R (see script). Relative abundances of guilds of fungi. Sites 1-3 were in the Lumbricus infestation; sites 4-6 were outside in otherwise similar woods. Comparison of relative abundances of guilds of fungi based on reads summed over infested and not infested sites. There were clearly proportionately more mycorrhizal fungi in Lumbricus-free plots than plots in the infestation. Monday, February 4 To do: Get going on AKES presentation. Arrange for return shipping of Betula specimens. I started work on revising my worm presentation. I am trying to determine which Eisenia species are present. Specimen/lot UAM:Ento:378050 is now identified as "Eisenia andrei and Amynthas," identified by Adrian Wackett by morphology. The specimen I collected from my compost pile recently (MOBIL8994-18, now also KNWR:Inv:35) was identified inconclusively as just Eisenia by BOLD's ID Engine. I read in Römbke et al. (2016) that these two species are separable DNA barcodes. I submitted the sequence from this specimen to NCBI BLAST and looked at only results that were in the Appendix of Römbke et al. (2016). This placed my specimen in the Eisenia andrei clade. Eisenia andrei specimen KNWR:Inv:35, live, 25.Nov.2018. I also updated the identification of specimen KNWR:Ento:6756 to E. andrei because the worms in my compost pile had come from the population at my parents' house. I later made this new identification unaccepted because vermicomposting cultures may contain both species (Domínguez, 2018). I need to look for E. fetida in these populations. I worked on revising my worm presentation on worms I gave in November, updating it with new information and modifying for the upcoming AKES meeting. I skied east across Headquarters Lake, the small lake to the east, and onto the PSDRA trail system. These trails had not been groomed. Upon a little searching on the internet, it looks like this organization is no longer active. Its website is gone and I saw no activities cited past 2014. Wednesday, February 6 To do: Finish AKES presentation. Finish travel-related arrangements. Get specimens together to take to Fairbanks. Fix akentsoc.org links and post meeting agenda. Arrange for return shipping of Betula specimens. My SLURM job on Yeti was canceled, again after six days. I do not know why. I will have to look into this later. I need to get my presentation done today. In looking through literature for my talk, I learned that there is another invasive species very similar to Lumbricus terrestris that I need to watch out for, Lumbricus friendi (see Csuzdi and Szlávecz, 2003). I attended the all employee meeting with the regional director and deputy directory in the middle of the day. I worked on my AKES presentation on worms.
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