Another month has slipped by without a weekly “weekly reads” post. Here’s an attempt to catch up!
Andy: I’ve read too much to cover in this post, but there were two issues that excited me the most. I mentioned one on Twitter:
Notable #scientists our grad students didn’t know: Dan Janzen, Lynn Margulis, V. B. Wigglesworth, Miriam Rothschild, N. P. Kristensen #sigh
— Andy Deans (@ardeans) December 2, 2016
I am seriously shocked by the lack of knowledge of our scientific history (some of these revelations came up during candidacy exams), and I fear that I have only myself (and maybe other instructors) to blame. I’ll have to do a better job of integrating an “entomologist of the week” exercise into ENT 432. And as a member of the curriculum committee I’ll see if we can figure out a fun and effective way of delivering relevant historical info to students in other courses. To kick off my thoughts I re-read this biography of Vincent B. Wiggleworth by Michael Locke (1996). Now that I am a PI I can appreciate the section about Wigglesworth as an advisor (The Teacher), which, unfortunately, sounds a bit too familiar.
My other historical discovery is that Stuart Frost was an avid cave enthusiast and helped resurrect the local caving club in 1950 – the Nittany Grotto. Seriously! I’ve been probing around the collection, especially our Rhaphidophoridae, Carabidae, and Pselaphinae, and sure enough we have lots of specimens from caves! I’m thinking about projects now, of course (because I don’t have enough … right), and started by reading this entire issue of The American Caver on Pennsylvania caves (check out page 24 for Frost’s article on cave insects!). I also checked out a metric ton of cave books from our wonderful libraries. More on this soon!
Emily: In working on a bioethics paper this week about the value of insects in the laboratory compared to in conservation and biodiversity projects, I read this paper about how we appreciate and recognize the value that insects play in conservation. Since I look at aquatic insects that could be potentially used as bioindicators, I know that it is oftentimes difficult to convince those who know little about your particular taxa of interest to care about their populations. Samways (1993) suggests that in managing an ecosystem, we must consider that even species commonly considered to be pests could be endangered. However, measuring exactly what actions can be taken toward which organisms, there is a need to understand the species in question-how it is interacting with other organisms and the environment, and how feasible it is to divert resources toward it. Furthermore, perceptions of insects also evolve, so priorities by funding/citizen science/other stakeholders may change due to research.
The week before I read a paper by Bush et al. (2016), who use the program AdaptR to predict the effect of climate change on 17 species of Drosophilidae in Australia. Niche modeling, though attempting to understand what is happening over time, often misses the fact that not only the environment is changing, but also the species is evolving. In this research, they attempt to understand the response of the flies physiologically and the subsequent impact of climate change on their dispersal. The models were able to predict habitat suitability for each generation of flies, which have 8 week life cycles. Through several different projections of models that examined the distributional response of the flies to six climate variables, it was found that species distributional ranges were predicted to decline, even though local abundance may not be. This is definitely something I think about when looking at numerous specimen records for a single locality-though at the micro level, a species’ distribution may look relatively strong in an area, but not in the entire range.
And prior to that I read a paper by Rach et al. (2008), who sought to determine if it is possible to use DNA barcoding to identify or discover species of Odonata.They looked at 833 species from 103 localities in the ND1 gene region to try and identify species using ‘characteristic attributes’ to distinguish taxa and build a tree. Here the researchers highlight the difference between pure and private CAs in delineating between clades. While for most insect taxa, CO1 is used for barcoding, the researchers used the ND1 gene region to identify between taxa. They found that it is possible to complement established species concepts with this data, but it can be tricky with higher level taxa to establish exactly what constitutes each unique category or group, but that simple synapomorphies can make it easier. Looking at the species and population levels of Coenagrionidae, it was possible to separate 13 species with character state as well as identify distinctive regional clades. This could be an interesting approach to determining larvae and matching them up with adults, especially since larval keys are not as robust for many taxa!
Carolyn: For our seminar on the evolutionary developmental biology of insects, I read a paper by Kamakura (2011) about a component of royal jelly, royalactin, which is responsible for causing larvae to develop into queens. Basically, caste differentiation in honey bees is controlled by the ingestion of royalactin, which acts similarly to epidermal growth factor. Something that stood out to me in this paper is that royalactin stimulates increase in body size, but it does this by increasing cell size, not the number of cells. This relates to our Malagasy paper (In press! Stay tuned), and also made me start thinking about what the advantages and disadvantages of each type of growth could be. Since royalactin is involved in ovary development, and since an ovum is a much larger cell than other cells, it makes sense that this method of growth would be selected for in this case.
Prior to that I presented a paper in this seminar, Kunte et al. (2014). This paper was about sex-limited wing patterning in a swallowtail butterfly species, Papilio polytes. This species exhibits sexual dimorphism where the female has a different wing pattern than the female. What makes this case even more interesting is that the female wing pattern mimics toxic species in the genus Pachliopta, whereas the males are not mimics. Previous researchers hypothesized that there could be multiple tightly linked genes controlling wing patterning, but the findings of this paper suggested that all of this could be controlled by one gene called doublesex. Doublesex (dsx) is a gene that is important for determining sex in early development, but the authors thought that this could also be the gene responsible for sex-limited wing patterning. Even though another paper published the next year (Nishikawa et al. 2015) showed that it was not dsx alone that controlled sex-limited wing patterning, it is still intriguing how one gene can play vastly different roles within development.
I’ve also been doing more reading on next generation sequencing (NGS). Last week I read a protocol that István sent me about library preparation for metagenomic sequencing of 16s. The 16s gene is about 1500 base pairs long, but there are different regions of this gene that are variable and useful for sequencing. The protocol was written for sequencing the V3 and V4 regions (about 460 bps altogether), but you can sequencing other regions using the same protocol as long as you have primers specific to those regions.
There are four steps overall for NGS given in this protocol:
1. Design primers.
2. Prepare the library sequences.
3. Sequence using MiSeq
4. Analyze the sequences using programs such as MSR or BaseSpace.
The protocol has a useful step-by-step, complete with safe stopping points and helpful tips. For example, when designing primers they recommend targeting regions that have a region in the middle of at least 50 bp in common across all of the sequences, since this makes it easier to align the sequences later. However, this makes me wonder if the primers we have already can be used, or if we would have to design and test new primers for NGS. Their section on preventing contamination is intimidating- apart from their recommendations of what surfaces to clean daily (basically every surface in the lab, including doorknobs and keyboards), they also suggest having complete sets of supplies devoted to each part of the protocol (i.e., different sets of pipetters for different parts of the procedure).