How-to – Dr. Julie V. Hopper

Population Genetics, Part III: Data Wrangling and Analyses

December 8, 2018December 9, 2018 by Julie V Hopper, posted in Uncategorized

So some good news!- My population genetics study on the two herbivorous biological control agents of water hyacinth: Neochetina bruchi and N. eichhorniae, was finally accepted for publication w/ minor revisions in Evolutionary Applications. I will certainly post it once it is In Press! This was one of the projects I did for my Delta Science Postdoctoral Fellowship research

So with that, I will fulfill my promise on posting Part III of my ‘how-to’ series for population genetics using microsatellites. To recap, Part I of this series explained what microsatellites are, and how to develop microsatellite markers, and Part II was on how to amplify and genotype these markers (the cheap way with universal fluorescent labeled tails, and multiplex pcr).

Part III (right here!) is my attempt to guide you through the jungle of population genetic analyses. I will discuss the main programs and analyses I used and how to properly format your data to make these packages and programs work!

NB_admixture_K2_K6 — STRUCTURE analysis of N. bruchi across eight populations and eight loci

I am not going to go into nitty-gritty detail because the tutorial for the ‘poppr’ package in R, does a FANTASTIC job on guiding newbies (including my former self) through the process of how to import data into R, exploring the data, and then how to conduct some basic and advanced analyses. The link is here http://grunwaldlab.github.io/Population_Genetics_in_R/index.html

Honestly- this is how I started learning how to conduct population genetic analyses in R.. I kid you not. I literally followed the above tutorial step by step and did almost all of the analyses just to get a feel for the data and how to run population genetic stats.

So- Where to start you ask?

Well, one of my collaborator/coauthors (Dr. Ruth Hufbauer-CSU) emphasized that before you analyze the data, a good first step is to know what your question is, and why you are asking those questions. Then you should base your analyses on those questions.

Here are some example questions:

Where did these samples/individuals originate from?
How many populations are there?
What is the genetic diversity in these populations, and are some populations more diverse than others? Genetic diversity is often based on one or more of the following: heterozygosity, allelic richness and diversity indices such as the Shannon, Simpson, or Nei)
Are there population genetic bottlenecks?
Is there inbreeding?
Are there hybrids (crosses between two species)?

Then of course you have to report some general marker- and population-based stats (Deviation from HWE- Hardy Weinberg Equilibrium, Linkage Disequilibrium (LD), overall expected and observed heterozygosity, (He and Ho), null alleles..etc).

Load the Data: Before you do anything, you have to load the data in a format that the programs recognize!

GenAlex- Excel Based Program-useful to check data formatting, and reformat data for import into R or other programs. However the main thing I found useful was understanding just what your dataframe should look like, which the Poppr tutorial emphasizes nicely: here
Adegenet package in R- (Jombart et al., 2010) Converts any type of data frame or matrix or txt file to a format that you need for a specific type of analysis
- For most of my data analyses, I used the following two formats, converting my csv to data that the packages could recognize, or that I could convert further:
  1. newdataname <- read.genalex(“datafile.csv”,genclone = FALSE)
    - you can convert this to a genepop format with the following code-
      - writeGenPop(newdataname, “newdata_genepop.txt”,comment = “blahblah”) #this function can be found here
  2. newdataname2=read.genalex(“datafile.csv”)
    - #need genclone for gytpes conversion, hence don’t use genclone=FALSE
      - gtypesdata=genind2gtypes(newdataname2)

Screenshot 2018-12-08 12.48.53.png — Example dataframe for import and analysis with the Poppr R package. Areas selected in blue represent the Loci, Samples and Populations, see poppr tutorial for further examples

Basic and Advanced Stats- I suggest to use:

Poppr– (Kamvar et al., 2015; Kamvar et al., 2014) this package depends on loading a lot of other packages and guides you through analyses in the tutorial. One example- is as a wrapper for the ‘vegan’ package- poppr calculates genotype accumulation curve (see if you sampled enough loci and individuals),
Pegas-(Paradis, 2010) -calculate Linkage Disequilibrium (LD) and HWE across populations for each locus
PopGenReport-(Adamack et al., 2014)- calculate null-allele frequencies pairwise F_ST and Jost’s D analyses, compare total and average allelic richness (accounting for sample size) and the number of private alleles among populations
diveRsity– (Keenan et al., 2013)-Estimate the average observed (H_o) and expected (H_e) heterozygosity, deviations from HWE (exact test) and the average ‘inbreeding coefficient’ (F_IS) for each population across all loci. In my paper I distinguish F_ISas a measure of increases in homozygosity due to genetic drift caused by a larger population being separated into sub populations, rather than due to consanguineous mating (Crow, 2010)
InbreedR- (Stoffel et al., 2016)-calculate g2 as a measure of inbreeding.

Hypothesis testing:

Linear Mixed Models, or Generalized (GLMMs) depending on which is more suitable for your data- with the lmer function in the lme4 package (Bates et al., 2015): I used this to test for the effects of population (collection site) on genetic diversity. Implementing an LMM accounts for the variability of the microsatellite loci by modeling locus as a random effect, and collection site as a fixed effect with allelic richness or expected heterozygosity as the response variables in separate models. Stepwise model simplification (Crawley, 2013) can be performed using likelihood ratio tests. Differences across collection sites can be compared, based on 95% CI, using Tukey’s post-hoc test in the ‘multcomp’ package (Hothorn et al., 2008). Read more about mixed models here.

Analyses of Population Structure

I suggest using several programs to see how they compare. I used:

STRUCTURE -as it is one of the most popular programs-(Pritchard et al., 2000). I used Clumpak (Kopelman, Mayzel, Jakobsson, Rosenberg, & Mayrose, 2015) to analyze the Best K, and to visualize and produce plots based on all of the runs from STRUCTURE outputs. Please see data-wrangling section below for more details on how to get your data into STRUCTURE, and also into Clumpak.
FLOCK- great program in excel (Duchesne & Turgeon, 2012), to see which populations are genetic sources for other populations, as well as determining ‘K’ the number of genetic clusters within a given population or site (useful to compare to output ‘K’s from STRUCTURE
‘adegenet’– to conduct Discriminant Analysis of Principal Components (DAPC) (Jombart, Devillard, & Balloux, 2010). There is a great tutorial here:

DAPC analysis on microsatellite data (eight loci) from eight populations of N. bruchi — Used the Adegenet package in R, and the Adegenet DAPC tutorial

Of course life is never easy.. especially when you have a MacOSX and for some reason the world revolves around PCs.

Here are some Data-wrangling tips for getting data into STRUCTURE and ClumpaK

To get my data into the STRUCTURE format, I used the function ‘genind2structure’ that I found online here. Then in R, I used: genind2structure(inputdata, file=”outputdata.txt”, pops=TRUE).
Following this , you will need to:
- DELETE THE GENALEX HEADERS
- GET RID OF ANY ‘_’ IN THE TEXT FILE
- GET RID OF LETTERS IN POP FILE, REPLACE WITH #S
- DELETE IND AND POP HEADER
- SAVE AS TXT FILE (TABS DELIMINATED)
- RUN PERL SCRIPT Below..
- since I have a MacOSX, I had to convert from DOS to UNIX with terminal program before loading in STRUCTURE by using similar code to this: while($_ = <>){s/\r\n|\n|\r/\n/g;print “$_\n”;}
  and you can find more info here .
- DON’T TOUCH FILE AFTER THIS.. TA DA!
- To get my files into the Clumpak web processor, I had to use a different zip-program (Zipfiles4PC) than what the MacOSx does, as for some reason Clumpak couldn’t process- Mac-zipped files.

Ok.. I think that is enough for now.. but really.. If I can emphasize one thing it is to go through the whole Poppr tutorial to get a handle of how to analyze data in R, and a feel for YOUR data!

Population Genetics Part II: Tips and Tricks, Multiplex PCR and Workflow of Microsatellites- the cheap way

April 13, 2018November 26, 2018 by Julie V Hopper, posted in Uncategorized

No this blog is not a belated April fools joke… there really is a method to save thousands of dollars on microsatellite marker multiplex and genotyping! If you are just reading my blog for the first time, this is Part II following up on my last blog: How-to use microsatellites for population genetics, Part I: Study Design, DNA extraction, Microsatellite Marker Design/Outsourcing.

When I first set out to work with microsatellites, I was on a budget and I had never had experience with multiplex PCR, genotyping or fluorescent markers before- so there was definitely an uphill learning curve.

To start (assuming you already have your microsatellite markers- see previous blog for this)- the next step is to order your fluorescent markers to see how things work in multiplex PCR. FYI-Don’t order your Liz Size Standard until you are done troubleshooting and checking things on gels because it expires kinda quick! Plus it ships really fast (at least if you are in the USA).

What are fluorescent markers you ask? If you look at the microsatellite genotyping peaks above, the different color peaks correspond to the different fluorescent tails that are ‘attached’ to the microsatellite primers. FAM= blue, PET = red, VIC =green, and NED = yellow. This way, you can see the different colors and know what markers they correspond to. The orange peaks are from the 600 Liz size standard which enables you to actually calibrate the size of the peaks. This is very easy if you use a program like Geneious as they have a microsatellite plugin. I will detail more of the data handling in Part III of this blog series.

Why multiplex PCR? Simple.. it is faster (& cheaper if you troubleshoot things quick).

Many folks use multiplex genotyping, where you do singleplex PCR with all the separate microsatellite markers, and then you add for example 4 non-overlapping microsatellite marker amplified products (from your singleplex PCR) into a well together for downstream genotyping (more on that process later). This process saves money, since instead of genotyping a single marker for 1$.. you can genotype 4 markers for 1$! However- singleplex PCR takes forever if you have a lot of samples and markers!!!! If you have 400 individual DNA extracts, and each sample requires 10 markers of genotyping.. this means 4000 PCR REACTIONS- YIKES- that would result in carpal tunnel in a heartbeat!

Multiplex PCR in contrast allows you to add 2-4, (or more) microsatellite markers with fluorescent tails into the PCR mix, making sure that markers with the same fluorescent tails don’t overlap in size (ie- a FAM marker amplified product of 100-250 bp compared to another FAM marker amplified product of ~300-400 bp size range- should be fine to put together in a mixture). Whereas you don’t need to worry as much if they are similar size but have different fluorescent markers (such as FAM (blue) versus NED (yellow)). There are pull-up issues, and inhibition issues.. but that is why you will need to test everything out first anyhow before running your final assays.

As for myself, two papers were key in learning how to streamline microsatellite multiplex and genotyping: Blacket et al. 2012 and Culley et al. 2013. Both studies utilized four universal fluorescent tails (different ones in the different studies)- so that all you need to do is to add the non-fluorescent tail (just the ATCGs) of the corresponding fluorescent tail (the ATCGs + the FAM, VIC, NED or PET fluorescent marker) to your forward primer, and then use pig-tails on your reverse primers (such as GT, GTT, GTTT- depending on your reverse primer). Cullen et al. 2013 has an appendix which actually walks you through every step, including the reaction concentration of each Forward primer +tail, Reverse primer +pig-tail, and Fluorescent marker +tail in the final multiplex mix. I ended up using the four universal tails in Blacket et al. 2012, and then used Culley’s reaction mixes.

Screenshot 2018-04-01 12.55.20 — Universal Tails used with PCR fluorophores, from Blacket, M.J., Robin, C., Good, R.T., Lee, S.F., Miller, A.D. 2012. Universal primers for fluorescent labelling of PCR fragments–an efficient and cost-effective approach to genotyping by fluorescence. Molecular ecology resources 12, 456-463.

Below is a great pictorial image of how this works (from Blacket et al. 2012)

Screenshot 2018-04-01 12.54.34 — Multiplex PCR with universal tails: Process from Blacket, M.J., Robin, C., Good, R.T., Lee, S.F., Miller, A.D. 2012. Universal primers for fluorescent labelling of PCR fragments–an efficient and cost-effective approach to genotyping by fluorescence. Molecular ecology resources 12, 456-463.

In addition to reading these papers (and their supplementary material) thoroughly, I recommend the following:

Talk to as many people as you can before you start/ while you are getting started -you always learn fabulous tips and tricks as well as what not to do!
Use the multiplex manager program -this will help you simulate what markers are compatible with each other based on the estimated product sizes, the melting temperatures (Tm) and the specific tails and flourophores you want to use. This will help you think about the different multiplex reactions that you can use.
Order the Qiagen Multiplex Plus Kit– this will streamline everything! I accidentally ordered the regular multiplex kit.. which is an older version and slower- so I had to stick with it once I got started. However- the Plus version enables you to use a faster PCR protocol! This kit is the same thing as their old ‘Type-it kit”, just better.
Order a set of just the universal tails without the fluorophores attached first, in addition to the forward primers with the universal tails, and the reverse primers with the pig tails. This will let you try running all the multiplex reactions out and test them on a gel to make sure you have everything working before you waste your precious flourophores which are expensive. This is also a cheap thing- 4x $6 max.. 24$ to try out a bunch of stuff before spending the big money is well worth it! By the way you will order all of your flourophores (reporter dyes) attached to the universal tail or the forward primer (the latter is a more expensive technique) from Thermo Fisher Scientific as they have patents on all of them except for FAM, which you can buy cheaper from Sigma or other companies (IDTdna, Elim BioPharm…etc)
When you have everything working (bands are where you expect them to be, and no large gaps between bands which indicate that the msat markers are targeting multiple regions of the DNA sequence rather than one region)- Then order black, sterile micro centrifuge tubes (this link is just an example- but any sterile brand will work)- this will be what you make all your fluorescent primer ‘party’ mixes in, which will protect the fluorescence from degradation- preventing you from having to order more and save you money and time!
Color code everything -from the tops of your individual fluorescent forward-reverse-fluorescent primer mixes (FRT: Forward-tail +Reverse-pigtail +Fluorophore-Tail) to your tubes with primer party mixes (all four FRT), to your multiplex pcr reaction mixes and to your excel files for the pcr-plates and genotyping plates.
Be organized when you pipette things onto your pcr-plate, and into your genotyping plate, see below image on how I organize pipetting into a pcr-plate, with the samples in the large tubes being moved in the order that I add things to the plate. I close the lid of each tube and move it to the upper tray after I add it to the plate so I don’t lose my place. I also use my tips from the box in order so that I can look at my tip-box as well to see where I should be.
Talk to the genotyping facility about if they permit a ‘troubleshooting’ run (free-of-charge) so that you can test the amount of final pcr product to add into each genotyping well. I used 0.5 ul pcr product (that had amplified products of four markers) with 11 ul genotyping mix (Liz size standard in Hi-di formamide)

Random Tips/Interesting findings:

The Liz size-standard has strict “keep in dark and don’t-freeze’ instructions when it is shipped to you. Be sure to put it in the fridge at 4 degrees and NOT in the freezer! Unfortunately it comes in a styrofoam box w/ ice-packs with no-outside labels instructing to not freeze…and so the mailing department or your lab technician might accidentally put it in the freezer (speaking from personal experience…)- The company (Thermo Fisher Scientific) was very nice in shipping me a replacement because of this issue. However… due to this occurrence I had the opportunity to test whether or not the Liz -size standard would still work when frozen for 6 hours, and when frozen for 24 hours….Results: The size standard still works great when frozen for 6 hours and for 24 hours ! With that said.. obviously don’t purposely test this, but if it is accidentally frozen- chances are you are still ok!
I also found that the Liz size-standard works great and is consistent for at least 2 months beyond its written expiry date…
- For both of these tests I had unexpired and unfrozen Liz-size standard to compare these tests to. No p-value available.. just my experience 😉
As for the genotyping- I used less Liz Size Standard than recommended (and so did everyone that I talked to). My specific reaction mixes were the following: 0.5 ul PCR product + 0.5 ul Liz Size standard, and 10.5 ul Hi-Di Formamide per genotyping reaction well. I know a lot of folks that use 0.5 ul PCR product + 0.2 ul Liz-size standard+ 9.3 ul Hi-Di Formamide.. and they have great success as well. I tried the latter mix and it worked, but because my pcr products had such high fluorescence (and I was over troubleshooting my primer fluorophore mix concentrations- I decided to instead increase my size-standard so that I could better separate the noise from the signals). My genotyping mix and final primer ‘party’ mixes result in the initial genotype peaks image of this blog- so you can see what I mean by high sample peaks compared to the size-standard.
As for the Hi-Di Formamide- I noticed that this does not have good results when you leave it in the fridge overnight and try to use it the next day for a second genotyping plate. However- I had good results with using Hi-Di Formamide that underwent 1-3 freeze-thaw cycles. Thus my advice is that you never leave it at room temperature or in the fridge if you have extra, but also to avoid too many freeze-thaws.
Additionally- Im sure you will find this out- but NEVER freeze your pcr-products after the multiplex pcr with the flourescent markers, or after you add the liz-size standard and hi-di formamide. If you can’t get your samples to the genotyping facility right away, then be sure to do a quick denature (95 degrees for 5 min) post combining the pcr product w/ the Liz size standard and hi-di formamide and then just keep in the fridge (and in the dark!) until the next day or two.

References

Blacket, M.J., Robin, C., Good, R.T., Lee, S.F., Miller, A.D. 2012. Universal primers for fluorescent labelling of PCR fragments–an efficient and cost-effective approach to genotyping by fluorescence. Molecular ecology resources 12, 456-463.

Culley, T.M., Stamper, T.I., Stokes, R.L., Brzyski, J.R., Hardiman, N.A., Klooster, M.R., Merritt, B.J. 2013. An efficient technique for primer development and application that integrates fluorescent labeling and multiplex PCR. Appl Plant Sci 1.

How-to use microsatellites for population genetics, Part I: Study Design, DNA extraction, Microsatellite Marker Design/Outsourcing

March 10, 2018March 10, 2018 by Julie V Hopper, posted in Uncategorized

So… you want to use microsatellite markers to assess the genetic variation and population structure of your focal study organism? Well if you are anything like me two years ago.. then you have no idea where to start. Otherwise- congratulations if you are already an expert- in which case you probably don’t need to read on 🙂

SeeHearSpeak — “See No Weevil, Hear No Weevil, Speak No Weevil” Illustration by Jacki Whisenant, contracted by Julie Hopper. Copyright 2017.

Two years ago, I was just like you (and these weevils above), and felt a bit overwhelmed and lost in undertaking the large task of designing microsatellite markers and genotyping these markers for the two weevils species (Neochetina bruchi and N. eichhorniae) that I have discussed in previous posts.

Very briefly to recap on my work: these two weevil species are used all over the world for the biological control of the invasive water hyacinth, including the Sacramento-San Joaquin River Delta, California. They have had variable success, with notable reduction of biomass and cover of water hyacinth in warmer climates compared to more temperate climates such as the Delta. Although temperature plays a large role in their success, I am also investigating the role of genetic variation and particularly whether there is lower genetic diversity and heterozygosity in the Delta compared to the native origin of these weevils (Uruguay and Argentina).

In Part I- (this blog), I will detail the how-to’s of sampling design and strategy, and the development of (or outsourcing) microsatellite markers.

In Part II- (next blog) I will discuss how to make your final microsatellite marker selections, and the workflow of multiplex PCR and genotyping.

In Part III- (come back in a month!) I will detail how to analyze the data with various R-packages and other computer programs, and how to format the data files correctly for these programs.

On this note, please research your study system thoroughly, as every organism is different and may require different sampling strategies and methods than I detail here for two diploid beetle species (Insecta). Additionally.. my overview below on Part I- is very brief and I definitely skip small steps to be succinct. Also my suggestions are not the only way to do things and below this blog, I post links to several other great resources. Lastly- This work is currently in prep for publication and I will post an update again after publication.

Part I:

Figure from: Grunwald et al. 2017, Phytopathology — Figure from: Grunwald, N.J., Everhart, S.E., Knaus, B.J., Kamvar, Z.N. 2017. Best Practices for Population Genetic Analyses. Phytopathology 107, 1000-1010.

Sampling Design and Strategy:

First before you start sampling or ordering primers- make sure that you have a solid study question with a testable hypothesis, and a good study framework.

Next: all of the power in your genetic analyses (aka, accuracy and ability to detect differentiation among populations, etc.) depend on: 1) your sample quality (aka DNA quality), the number of samples (replicates) per treatment or location, 2) the number of high quality microsatellite markers (e.g.quality relating to two important characteristics: markers are polymorphic -having 2 or more alleles per locus-with more being better, and the markers lack true null alleles), 3) the robustness of your PCR – whether the PCR conditions are truly suitable for your markers, and whether they can result in reproducible data, 4) the assumptions of the data and 5) the choice of statistical tests and whether the tests are truly suitable for the data.

I will cover the latter (regarding statistical tests) in a future blog, but for today I would like to focus on the ideal # of samples and the # of polymorphic markers. There has been debate about how many samples and how many markers are necessary for robust studies, and if you study an endangered species -sometimes you just have to work with what you got!

In a perfect world– you will want to make up for what you lack in samples with microsatellite markers (loci) and vice versa. So if you have a lower end of replicates, then you will want a higher number of microsatellite markers (# of loci, and more important is to have polymorphic loci with 2 or more alleles/locus) to test for each individual (replicate), and again vice-versa. There are a couple great papers that discuss sampling strategies and study design that you should definitely check out, particularly the one noted in the figure above (Grunwald et al. 2017), as well as Hale et al. 2012 which states that 25-30 individuals per population should be sufficient to accurately estimate allele frequencies given population (with some caveats). Caveats being that obviously, 25-30 individuals per population would likely NOT be enough if you only have four microsatellite markers, particularly if these markers are not polymorphic or very variable (variability referencing to the # of alleles per locus- the more the better!).. so keep this in mind. In general, with that many samples- 10-15 polymorphic markers should be fine (although the more the better), but again this depends on your study question and study system. Also, more samples might be necessary if you are interested in population differentiation (population genetic structure). In fact, in a landscape genetics study, Landguth et al. 2012 demonstrated that increasing the number of loci (and particularly having more variable loci) is more likely to increase the power of population genetic inferences compared to increasing the number of individuals.

You can also test your samples with genotype accumulation curves to see if you have captured the majority of genetic variation (I used the poppr package in R for this and will discuss more on poppr and its primer in Part III of this blog series).

With that said.. If I would have known 1 year ago what I know now…. I would have asked for folks around the world to collect more weevils for me, and I would have extracted more DNA! Just remember.. not all of your DNA extractions are going to end up working out..due to various human error and/or preservation issues. Thus its always good to add at least 10-20 more samples than you think you need!

map_with_labels_pop_gen — Sampling locations of *Neochetina bruchi* and *N. eichhorniae* individuals that I used for the focal population genetics study (Hopper et al. In Prep). Thanks to all those who sent me weevils!

Designing or Outsourcing Microsatellite Marker Design:

Marker Outsource Options: I want to first be upfront in that I actually ended up outsourcing this component of my study as I was going through a tough time and taking care of my dad who had metastatic cancer via at-home hospice care in Columbus, Ohio for two months. Needless to say- I was working remotely then, which made the decision to outsource this part of the lab work an easy decision. I researched a lot of outsource options and in the end I went with the cheaper and most recommended option by several colleagues- the Savannah River Ecology Lab at the University of Georgia. In the end I have mixed opinions on their work and please email me if you would like more info and I will detail the ups and downs.

Brief Workflow for designing microsatellite markers:
1. First! Check the literature to make sure microsatellite markers have not already been developed for your species or a sister species (the latter of which will sometimes work). Using previously developed markers is obviously the easiest and cheapest route!
2. If the markers have not already been developed: Obtain high quality and high molecular weight DNA Extractions. I love doing 5% Chelex DNA extractions, but the resulting DNA can be full of PCR inhibitors- so I always use the second half of the DNAeasy kit to purify and clean up my DNA samples. You can also buy replacement spin columns for these kits way cheaper from Epoch Life Science. Then quantify them on a nano-drop or a similar DNA quantification instrument and additionally run them on a gel to make sure that you have ≥100 uL of ≥50 ng/uL of >10kb DNA per sample.
3. Send to a sequencing facility (Illumina with paired ends >150bp preferred)
4. Clean up sequences/fix Errors and Run a program called “Pal_finder”, or use a similar program. Pal_finder can analyze 454 or paired-end Illumina sequences ( ~150bp from each end). This program sends possible primers to Primer3 for primer design and searches for how often each primer and primer pair occur.
5. Filter the resulting data set by only including: a) sequences for which primers can be designed (e.g. enough flanking sequence) and b) primer pairs that occurred 1-3 times. Then, sort by motif length (di, tri, tetra, etc.) to quickly find tri or tetra nucleotide repeats and look to see if the motif was found in both directions of the sequence (which can be bad as they typically end up being smaller PCR products, but this depends on your goals). Finally, order a bunch of the primers that look promising-say 48 primer pairs to start, and test them out on a subset of 24 individuals, with an equal distribution of these individuals across all your study locations, or select individuals that you think will have a lot of variation. See Initial PCR testing in the next Blog.

To be continued…

References

Grunwald, N.J., Everhart, S.E., Knaus, B.J., Kamvar, Z.N. 2017. Best Practices for Population Genetic Analyses. Phytopathology 107, 1000-1010.

Hale, M.L., Burg, T.M., Steeves, T.E. 2012. Sampling for microsatellite-based population genetic studies: 25 to 30 individuals per population is enough to accurately estimate allele frequencies. PloS one 7, e45170.

Landguth, E.L., Fedy, B.C., Oyler-McCance, S.J., Garey, A.L., Emel, S.L., Mumma, M., Wagner, H.H., Fortin, M.-J., Cushman, S.A. 2012. Effects of sample size, number of markers, and allelic richness on the detection of spatial genetic pattern. Molecular ecology resources 12, 276-284.

Helpful Resources on Getting Started for Part I

Lecture on Intro to Microsatellites

How-To: Stage-Structured Matrix Models

November 22, 2017November 29, 2017 by Julie V Hopper, posted in Uncategorized

Happy Thanksgiving everyone!

So this week I constructed several stage-structured matrix models- aka Lefkovitch models- to estimate the finite and intrinsic rate of increase of the weevils Neochetina eichhorniae and N. bruchi under laboratory simulated Fall and Winter conditions in the Sacramento-San Joaquin River Delta. This work is in conjunction with a postdoctoral researcher- Angelica Reddy and Paul Pratt’s laboratory at the USDA to test the temperature performance of these biological control agents.

As you know, if insects are adapted to warm weather- they don’t perform very well in colder temperatures and this can be very applicable to biological control agents (such as the two Neochetina weevil species) that are brought from their tropical origins to colder regions to control invasive species. Below is a cute cartoon I had a scientific illustrator Jacki Whisenant draw for me, and for a new children’s book we are writing…stay tuned!

ChillyWeevil — Copyright 2017, illustration by Jacki Whisenant and made for Julie Hopper

Because we are working in the laboratory on these two species we are able to gather a lot of life history parameters of the weevils undergoing Fall and Winter conditions. These parameters include: development time and survivorship of the different insect stages (egg, III instars of larva, pupa, pre-reproductive adult and reproductive adult), as well as the emerging sex-ratios, and longevity and daily and lifetime fecundity of the reproductive female adults.

From these parameters we can conduct several different analyses to approximate the finite rate of increase, intrinsic rate of increase, generation time, doubling time and net reproductive rate of a species to understand more about their potential population growth rates (which of course is important for biological control).

My favorite way to approximate these population growth parameters for insects is to use a stage-structured matrix model (Lefkovitch model). There are other methods you can use as well- but I won’t go into that here. If you would like to read more see the citations at the end of this blog.

Instead, I will provide a how-to tutorial since while I was working on these matrix models as a graduate student- I realized there is a lack of tutorials on the web on how to construct these models in an intuitive manner. I got lucky as both my PhD adviser and one of my lab mates (whom had already done the research on stage-structured matrix models) helped me understand how to construct and interpret the models. In the name of paying it forward- I am attaching here an excel worksheet that has all of the calculations and formulas that demonstrate how to construct these stage-structured matrix models (see link).

Julies_tutorial_example_matrix_for_popbio

In my next blog- I will detail how to use this resulting matrix and input it into the package popbio (Stubben and Milligan 2007) for calculation of finite rate of increase (lambda), intrinsic rate of increase (r), doubling time, generation time, net reproductive rate and much more!

Disclaimer- this is for insect stage-structured matrix models only as calculations differ for plants and vertebrates typically.

Here are some of the calculations that are built into the excel formulas:

Below is another screenshot of the file:

Below is a diagram from the famous study on Loggerhead sea turtles that explains the flow of this matrix better. However be aware that the matrix above and in the attached excel sheet-calculates gamma as 1/duration which is very different than the famous example on turtles (below), and from any matrix with plants- mainly due to life history differences among plant, invertebrates and vertebrates.

Screenshot 2017-11-22 13.10.04.png — A Stage-Based Population Model for Loggerhead Sea Turtles and Implications for Conservation Author(s): Deborah T. Crouse, Larry B. Crowder, Hal Caswell Source: Ecology, Vol. 68, No. 5, (Oct., 1987), pp. 1412-1423

References

Caswell H (2001) Matrix Population Models: Construction, Analysis, and Interpretation. Sinauer Associates, Sunderland

Crows DT, Crowder LB, Caswell H. 1987. A Stage-Based Population Model for Loggerhead Sea Turtles and Implications for Conservation. Ecology, 8, (5): 1412-1423

Stubben CJ, Milligan BG (2007) Estimating and analyzing demographic models using the popbio package in R. J Statist Software 22:1–23. doi:10.18637/jss.v022.i11

Resources:

Awesome powerpoint by Chris Free at Rutgers

Another awesome tutorial on primarily the Leslie matrix from UCSC

How to Get into Grad School: Part I

September 29, 2017October 3, 2017 by Julie V Hopper, posted in Uncategorized

The past month has been crazy again (or maybe this is just how I start all my blogs?).

My husband and I made the big move to Los Angeles as he started his PhD program at the University of Southern California (USC). In-between moving, I’ve been driving back and forth between LA and the Bay Area to finish up my lab work for my current postdoc position so that I can get all of my data and remotely work the rest of the year in LA.

When Im not in the Bay Area living the couch surfing and pipetting life style, I’ve been surveying my favorite coffee shops in the West-Adams area (so far Nature’s Brew and Cafe Ignatius are the winners!) and submitting postdoctoral research proposals for several fellowships as well as applying for jobs.. real big time professor jobs!!! Fingers crossed that something comes out of all of this!

However, while I was working on all of my research and teaching statements, I realized that it might be useful if I posted a blog on the how-to’s of graduate school.. since I have now successfully put that behind me.

For Part I, I will focus on just the ‘admissions’ aspect of graduate school.

I will have a Part II later on with details on how to succeed and survival it all.

Disclaimer: This advice mainly pertains to PhD programs and STEM fields, and may differ slightly if you are applying for a masters degree or other programs (non-STEM).

Part I: How to Get Into Graduate School

A: What to do as an undergraduate to prepare for applying for Graduate School?

EXPERIENCE EXPERIENCE EXPERIENCE! Get involved in whatever research opportunities that you can. Don’t be too picky if it is your first research experience, since opportunities lead to more opportunities and every opportunity will give you a little bit more insight on what you are passionate about. Furthermore.. every research project should have the same fundamental scientific process (or it should anyhow) and so you will learn about science and how to conduct research by taking advantage of research opportunities that are available. After you have a little bit of experience, try to conduct your own independent projects either in a class setting, under the mentorship of a professor, postdoc or graduate student and/or apply for undergraduate research fellowships.

MAKE CONNECTIONS WITH PROFESSORS & RESEARCHERS- In addition to going to office hours and talking with researchers at your University, research experience will also help you establish real connections to professors, postdocs, and graduate students. Connections are critical for meaningful letters of recommendation, as well as getting advice on your next steps, regarding what research programs, advisers and universities are a good fit for YOU!

GRADES AND GRE SCORES…do they matter?

Short answer: Yes, but don’t kill yourself over it. Long answer: As long as you don’t have horrible grades and GRE scores (e.g. B’s are fine, and being in the average range is fine), your research experience and personal character will be just as important to the graduate admissions committee. Regardless, since you still have to take the GRE for most university programs, start studying at least 6 months in advance of your test date.

B: How the Heck do you Choose a Graduate Program and/or Adviser?

Figure out what you are passionate about!!! Think about what research projects and what types of courses inspired you? The ones you liked studying for? Maybe this is a clue to what you are passionate about!Hopefully your research experience and courses as an undergraduate can give you a head start on this critical component. If you need more help on finding out what really moves you- go to your school library and sit down with some various peer-reviewed research journals (Science, Nature, Ecology, PNAS, etc) and browse through them until a topic hits your interest. You can also browse an Internet research browser such as ISI web of science, but this is a bit harder if you don’t know where to start!
Do you have any location limitations for graduate school? Write out a list of places you would be willing to live (or not to live in).
Browse the faculty members and their research profiles at prospective Universities that you would like to go to.
1. Look at their CVs, and the publications they have produced
2. Look at how many graduate students they have mentored and how many students have graduated.
3. Read several publications and see what they are currently working on.
4. If any of their research interests you: EMAIL THE PROFESSOR!!
Email the Professor of interest and think about Applying to the University

The email should go something like this: (substitute specific and personal items for XYZ)

Dear Professor XYZ,

I am very interested in your research on XYZ because I have experience with xyz ….. I read your article entitled “XYZ” and was particularly intrigued in the fact that… ……I would love to focus on this research area for my PhD at the University of XYZ in your laboratory. Would you have any time to discuss the potential for working in your laboratory? If you do not have available funding or positions, would you be willing to work with me to apply for funding or able to recommend another laboratory in this field of research?

I have also attached my resume for your review.

Thank you for your time, XYZ

Email a ton of other professors as well (don’t put all your eggs in one basket!)
Look at other research profiles at various Universities
Think about possible grant-writing opportunities and come up with a rough-draft proposal if you think you need to take this direction.
Email professors again (in two weeks) if they haven’t responded.
Don’t take a lack of response or rejections personal
Schedule interviews (phone, Skype or In-Person) for yourself with the professors you emailed if they respond positively. I actually scheduled my own meetings with professors I wanted to work with at UC Berkeley since I was in town for a week coincidentally, and I think that helped!

5. Have an Interview?! Dress nicely (even in on the phone!) be on time, and come prepared (e.g. read all the papers you can in the area of research you plan on discussing with the Professor.. particularly the articles the professor authored!). Provide your thoughts on some of the theory in the field and ask lots of questions.

C: How do you apply to a graduate program? and When?

****Establish Connections****Hopefully from the above, you can see how important it is to establish a connection with one or more professors from the program and university of your interest.

PUT A LOT OF EFFORT INTO YOUR PERSONAL STATEMENT and/or STATEMENT OF PURPOSE: You should be passionate about something and this should be very apparent in your statements. Be careful and stay honest. Don’t say you have experience with things that you don’t, and don’t propose an area of research that you are not interested in. Also, if you are interested in Ecology, Evolution and/or Environmental Science- it is beneficial to list specific faculty that you have already made contact with, and state how your interests align with their research. For MCB/Chemistry and maybe some other departments- my understanding is that they mainly do lab rotations, and so you would want to list several faculty at least.

For your personal statement, let the admissions committee see who you are as a person, and how this has contributed to your passion in the field that you are applying to. What sets you apart from others? Bring in your personal story- how you grew up, your cultural and economic background (the latter only if you had disadvantage and you overcame it).

These statements are tremendously important, so proof read your statements (grammar/spellcheck!). Send your statements out to former grad students, postdocs and faculty that you worked with during your undergraduate years for more feedback. Don’t forget to tailor the statements to each of the schools you are applying to and be careful if you are copying and pasting to not list a different school for the current school you are submitting your essay to.

Do not underestimate the power of these statements.

Timeline: You should be studying for the GRE’s around June-August, Take the GRE early in case you need to retake it, make contact with prospective advisers/labs around August-October, working on your statements in November/December and applying for Schools in December/January. * Note this is mainly from my experience with schools in the USA and may vary across the globe.

D: Congrats- you got in to multiple places! How do you choose?

If you get into multiple places- make sure you visit each University and each prospective lab that you would want to work in. For the University level: Do you like the location? e.g- would you be happy with climate and surrounding area? Does it suit your personal life? e.g. If you have a partner- how do they feel about relocating to that area? How does the University compare to your other options in terms of reputation and funding?

For the Department Level: What is the funding situation like? How much money will you make and is it enough to live off of in the surrounding area? Do you need to teach? If so how much would you teach? Teaching is great, but you don’t want it to interfere so much with your research that it takes you 10 years to graduate! Will you have health insurance? How are the benefits compared to your other options? Also- how is the social culture in the department? Do faculty, postdocs and graduate students all work together well? Are there at least some social events that the Department hosts? Do graduate students seem happy? What are the career support options? (eg. do they have a career center or folks that can help you with job applications when the time comes?)

Lastly and perhaps the most important: At the Lab/Adviser level:

What is the adviser like? Is he/she hands-on or hands-off? Which of these suits you best? Are there lab meetings or does the professor (adviser) schedule one-on-one meetings with the students? How available is the professor? e.g. – Are they chair of the Department? If so then just keep in mind they might be more busy than other professors and might be more hands-off while they have that position (doesn’t always hold true, but something to ask them about at least if they do have a demanding position).

Are the graduate students in the lab relatively happy and productive? Have the graduate students published papers in a timely manner? Have former graduate students secured relevant jobs (government/academia/biotech)? Does everyone in the lab seem to work well together?

What are the laboratory facilities like? Do you have access to all of the equipment/materials that you need (either in the prospective lab or in willing labs nearby?) Are things relatively organized, clean and safe?

Does the research still interest you when compared to your other options? Lastly- is the research in an area of high funding? This might be important if the Department can’t pull together enough funds for your research or stipend.

Weigh all of your pros and cons and then go with your gut feeling! Good Luck!

Traveling in Cuba as an American

July 31, 2017September 27, 2017 by Julie V Hopper, posted in Uncategorized

Cubacarte2015 — *Photo from cubacasas.net*

I haven’t posted for awhile as in addition to recently getting back from our 10 day honeymoon in Cuba (followed by a cousin’s wedding in the DR)- we are preparing to move to LA (my husband is starting his PhD program at USC soon)! This past month has been a whirlwind- but all in all a good time and Cuba was certainly an adventure (complete with ups and downs!).

Cuba isn’t one of those places you go to just flop down on a beach chair and drink all you can drink piña coladas while you relax. In my opinion -Cuba is a place you go to understand and appreciate the culture, and to learn more about how a socialist society operates.

I’ll detail our trip in my next blog- but first here is some of my advice, How-tos, and insights on traveling in Cuba.

You have to designate your travel under one of the 12 reasons for travel.
- We went under the “People to People” travel which falls under the ‘Educational activities and exchanges’ category I believe. We were required to keep a journal documenting our daily activities and exchanges with the Cuban people. We did things like teaching capoeira to Cuban children in Habana, Beach Cleanups (and talking to the locals about the trash on the beaches), and just talking with everyone that we possibly could (taxi drivers, airbnb owners, shop owners, musicians, folks walking on the street, etc. ) Note- travel is subject to change under the new rulings under thou who shall not be named, but you should be good to go in the next couple months still and see more details here if you plan to fly via Southwest like we did
You should pre-budget everything and bring all cash with you (Euros or Canadian dollars are best). American credit cards/debit cards don’t work. Really.. I tried. I even called Navy Federal Credit union which allows for cards to be used in Cuba… but looks like Cuba still didn’t let my card go through regardless. Don’t bring US dollars because Cuba charges you 10-13% for exchanging Dollars for CUCs… Just bring EUROs and you will have an easier time. Also bring about 200 EUROs more than you think you will need… more on that later.
If you want to travel around cheaply- reserve a Viazul Bus about 10 days ahead of time online. Or you should plan on getting lucky hitchhiking, taking a local taxi ‘collectivo’, or paying a ton of money out-of-pocket for a tourist taxi. (I’ll write more about this in my next blog …ugh).
Practice your Spanish before going if you are not fluent already. I speak portuguese and had a decent enough vocabulary in “Portenol” to get around and have conversations with folks- and it helped us out a lot. I used DuoLingo to brush up before I left.
Airbnb reservations are likely the best way to reserve places for Americans. This and online reservations with anything really will help with lowering the amount of cash you carry on you while in Cuba. Many Cubans rent their “casa-particular” out with personal websites, in-person advertisements in Cuba, and on Airbnb. Typically the Airbnb rates are a bit more than what you would pay in-person, but again the online pre-pay feature of Airbnb is worth it.
There are two currencies in Cuba: Cuban Pesos (CUP) and CUC. Pesos are worth way less than CUCs (25 CUP is worth 1 CUC about). Don’t exchange money with people on the street- this is the easiest way to get scammed, as they can hand you back pesos instead of CUCs for your Euros. See photos below. Keep in mind there are coins also that differ between these currencies but look similar to a new tourist.
The down-low on food:
- Do Not expect great food at hotels/resorts. Your best meals will likely be at the most random unexpected places, and not necessarily in your Cuba Guide Book. We stayed at the Maria la Gorda Hotel for three days to go scuba diving and have time at the beach, and the buffet breakfast was not good. They tried their best, but the unfortunate truth is that the government limits how much hotels and resorts can obtain/spend on food and facilities. We did find that the shrimp at their dinner restaurant was great!
- The best food we had was: eating fresh fruit from the local market (pineapples and large mangos are 10 pesos each (CUP) which is almost 1/3 of a CUC, avocados are 8 pesos and limes are 2 pesos), fresh bread from the bakery (price varies depending on size of bread- but about 10 pesos will get you enough bread for two people), and fresh eggs (10 pesos each) from the egg man (notice how there are little shops for everything). A full and large breakfast (eggs,bread, fresh fruit and coffee) for two people was less than 2 CUC. You can also just grab an egg and bread sandwich for 10 pesos from a street corner ‘cafeteria’.
- And the best restaurant we ate at was actually someone’s house. We ate on the footsteps of this woman’s (Cari) house in Habana Vieja. Beans, Rice, Fried Chicken and Salad for 30 pesos (about 1.10 CUC which is about 1.10$ Us dollar)… It was fantastic, not to mention the amazing sights and sounds of the neighborhood coming alive in the evening. The address for her restaurant/house is: 105 Santa Clara, Habana Vieja Cuba. Below is a picture of me and Cari in her house after a wonderful meal. She even wrote me out the recipe for the Cuban Beans and wouldn’t even accept a tip after we came back the second night. You have to go here and have a meal and tell her that Julie and Gerid recommended her restaurant. And no we did not get sick.
  Cari and I at her restaurant: 105 Santa Clara Ave, Habana Vieja, Cuba
Bring a water filter! We brought this gravity-operating water filter (gift from my cousins!) and hardly ever bought water. Although the water in Habana (Havana) is supposedly safe for tourists we did not try it and did not meet any other tourists that tried it either. However after seeing all the construction going on and pipes being worked on- I’m glad we did not try it. We saved a ton of money and did not get sick from the water we filtered (I did get sick however from eating an egg-sandwich at the Jose-Marti Airport.. ugh).
Souvenirs: Make sure your artwork comes with a valid certificate (otherwise you will pay 40 CUC at the airport for it). We paid 45 CUC including the certificates each for two nice and large paintings. If you buy cigars on the street (not recommended, but if you have someone trustworthy then it is cheaper than the factory)- make sure that the cigars have a seal on the box so that you can take them home.
Racism exists in Cuba… but most of the light-skinned Cubans will deny this. Not all Cubans are racist by any means, but my husband (who is African-American) was treated miserably by our first Airbnb host lady, and was stared at on the street a lot by many Cubans (and no it wasn’t because they couldn’t believe how handsome he is). For example-our first airbnb lady made breakfast for us everyday and was super nice to me, but barely looked at my husband in his eyes and couldn’t reply hello or goodbye to him most of the mornings (and she spoke perfect English). My husband and I weren’t the only ones to notice the covert racism. We went to this amazing ARt/Music/Dance collective: Fabrica del Arte in Vedado, Habana (a must-see if you visit Habana!)- and were struck by the art piece below. We even had a conversation with a local Afro-Cuban that was so ecstatic that finally someone was conversing about the issue of racism in Cuba.
My husband and I mad about racism in Cuba.. this piece of art at the Fabrica del Arte Cubano (FAC) in Vedado, Habana, Cuba depicts this perfectly.
Scams are everywhere and are incredibly annoying: Some of the scams that we encountered (and did not fall for) were: 1) overpriced taxis, 2) currency exchanges on the street –and giving you back pesos instead of CUC (see above note on the currency), 3) ‘The Cigar Festival’... People will tell you ‘its the last day for the cigar festival, you should go and get good prices on the cigars’.. we never went to check it out but we know it was a scam because four days later someone said “today is the last day for the cuban cigar festival”..ugh!, 4) overpriced paintings that are not certified (They try to sell these paintings for 130 CUC instead of 45-60, and then in addition to that they do not have the certificates and lie to you saying that the certificates are 40 CUC… The truth is that the certificates are only 2-3 CUC, and if you don’t get a certificate with your artwork, then you will have to pay 40 CUC at the airport. My husband and I had two main rules to avoid scams: Do not let anyone lead you anywhere, and do not agree to anything right away. Just tell them thank you and that you will check it out later. That will give you time to research whatever it is they are trying to sell you and discuss the pros/cons.
Online Cuban agencies will likely rip you off. We used the CubanTravelNetwork to book our Maria la Gorda hotel and scuba diving (to not have to bring as much cash with us once we were there)- and they majorly ripped us off on the scuba diving packages. We overpaid them for scuba diving compared to what the hotel charged in person, and then on top of it our scuba diving equipment was not even included (which they did not tell us during the online purchase)- so we had to pay for that in person which we did not budget for.. ugh.
Segregation of tourists and locals exists everywhere from the taxis to the Coppelia ice cream place (Vedado, Havana, Cuba). They have security guards which actually force you to go to the tourist sections of the ice-cream parlor (where they charge you more money). No thank you. In the end, we got our ice-cream at a small spot in Vedado for < 1 CUC each elsewhere. I’m all for giving to the local Cuban economy, but I prefer to do it via tipping rather than segregation.
Socialism: Yes it is a socialist country- and it is evident in the fact that even the poor people are well taken care of in terms of housing, food, water, health care and education. I only saw one homeless person the whole 10 days we were there, and even all of the stray dogs and cats were fed every night via food on cardboard paper (I’m not sure who went around feeding them at night). I think this is also why all of the strays were very nice and well-behave. However, in my opinion- if you want anything aside from the basic necessities- it is hard to do so in Cuba (unless you have family sending you money, or an extra house you can rent out as an air-bnb/casa particular). We did meet some people who felt trapped by the system. The government has a lot of control on everything- evident from the rationed food at hotels/resorts, and from the fact that if you are born in the east of Cuba you cannot immigrate to Havana unless you become a police officer (thus many folks seek out that job). Coincidentally (or not) eastern Cuba is also the more Afro-Cuban region… again.. racism is very apparent in this country.

Happy hairless dog

Well fed strays
The Environment: I was a bit surprised when I got to Cuba because I had heard so many good things about all of their marine and land preserves, and about their efforts to preserve the environment. I did in fact go scuba diving in one of the marine reserves in Maria La Gorda- which was spectacular (lots of live corals and fish while scuba diving), but I was disappointed by all of the trash on the beaches, and even one of the scuba diving instructors threw his cup overboard on the boat ;(. The snorkeling was only so-so however at Maria la Gorda (lots of dead coral), but had some fish, and new coral growth on the docks was apparent. There are lots of land and marine reserves in Cuba.. it is true and these reserves are beautiful from what I saw, but in my opinion littering is a huge problem for Cuba. There was trash everywhere we went– from the streets in Havana, to the Malecon (a strip along the ocean in Havana), and on the beaches. Not to mention the fumes from all of the old cars. However in contrast, I did see a public outreach center in Havana about preserving native species, and the negative effects of littering, fumes from cars, and invasive species. So one can only hope that more public outreach and education will preserve Cuba’s natural beauty. Speaking of invasive species – I did see water hyacinth in Pinar Del Rio, Cuba! I wasn’t surprised though since I knew that biological control using the weevils (Neochetina spp.) has been used in Cuba for controlling this invasive weed.

All in all, I still immensely enjoyed our trip in Cuba- and definitely saw some of the positive aspects of a socialist society. I fully recommend visiting Cuba, and experiencing it for yourself (Just bring enough money!).

View of Havana, Cuba from ‘El Morro’ on our last night

Academia and Work-Life Balance

June 27, 2017June 29, 2017 by Julie V Hopper, posted in Uncategorized

fwp-A-Healthy-Work-Life-Balance-web In Academia, there is often a lot of chatter and inner-struggle concerning the ideal Work-Life Balance. Although it may be too early for me to comment on this (since I’m only a postdoc and I don’t have kids), I feel that I have a decent work-life balance. After all, I finished a PhD program with both my physical and mental health intact afterwards- so here goes some of my opinions on this much sought after balance.

First off – let’s address the statement “Academics are Work-A-Holics”:

I always hear folks (including academics) complain about how academics work all the time. I experienced this firsthand since I grew up in an academic household and I saw how much both of my parents worked (my own dad even labeled my mom as a ‘work-a-holic’). Both of my parents are/were tenured professors and scientists, and my mom was Departmental Chair at one point at the Ohio State University.

I also saw how much my parents (and other academics) enjoyed their work, which I think is one of the main reasons of why academics ‘work’ a lot. I will linger on this for a second– because: if you enjoy your work – is it truly ‘work’? Is this any different than an olympic athlete that trains constantly to achieve their goals/dreams? (Don’t worry.. Im still going to talk about enjoying life below this also).

The concept of enjoying your work, and waking up excited to start your work day is more than most people outside of academia can say about their jobs. And yes, I realize that academia is a privileged job position to hold because of this very reason.

However even though academics self-identify as work-a-holics- I also see and appreciate the huge amount of flexibility that academics have for when and where they choose to do their work. My parents for example always made time for all of the important things- my gymnastics competitions, birthdays, family vacations… the list goes on, and of course they could take off work whenever I got sick. When one parent was writing a grant- the other parent would take me to a bookstore or to the amusement park (weather pending). My dad was actually the main chef, and we would have family dinners together almost every single night!

Now compare this lifestyle to the working family where both parents hold down more than one full or part time job… Or to a family of lawyers or doctors.. or business CEOs….How many family dinners do these families have? How many times are they able to take off work without penalties for when their kids get sick or have a special event?

If you keep this perspective – then maybe you will see my first main point.. that academia might actually be the most perfect job (if you can get a tenure-track position of course) to feed your soul and to have a decent work-life balance (with a little bit of effort of course).

In fact for me this hit home when recently my dad got terminally sick during my postdoc (metastatic cancer from a brain tumor) and I was able to work remotely in Ohio helping my mom provide at home hospice-care for him for almost two months! Although it was horrible watching my dad suffer, as well as knowing what was to come, I am so glad I was able to be there with him and my family during his last months.

How many other jobs would let someone take off two months and work remotely? Not many I bet. I also had a ton of support from colleagues and my research mentors which makes you realize that most academics are amazing humans and care about each other’s well being.

So, given that academics have a soul-fulfilling job (ideally), and have the flexibility and potential to have a decent balance….

How do you ensure a work-life balance to where you make time for friends, family hobbies and a healthy life-style?

Below are some of my tips that I have implemented myself. *Disclaimer- I do not have kids.. so the below tips could likely very well change or be different for those that do have kids.

1. *MAKE* THE TIME FOR THINGS IMPORTANT TO YOU

Aka- Don’t try to ‘find’ the time… Just ‘Make’ the time and stop making excuses.

Example- if exercising is more important to you than the postdoc or faculty happy hour.. then go exercise! Better yet if you can find a colleague or friend to exercise with.

This theme is incorporated in all of the other tips below.

2. BE PRESENT IN WHAT YOU ARE DOING AT THE MOMENT

Whether you are working or relaxing/having fun- try to be present in the moment.

This advice goes hand in hand with #3 below.

There is no point in taking time off of work if you are thinking about work- so face the fact that in that moment you are not supposed to be working and just enjoy the time. In contrast- if you are working- don’t go on facebook or do other non-work activities. Try to keep to the task at hand.

phd101215s

3. USE YOUR TIME WISELY

I’m sure you have heard that ‘Being Busy is Different than Being Productive‘. Sometimes the hours that you spent working in a day don’t always equate to ‘productive’ hours.

By this, I am not discrediting the creative process or troubleshooting projects, which can sometimes feel unproductive.

However, just be aware of your time spent ‘working’ and how productive you are actually being while away from your other activities/spending time with family/friends.

For instance- I find that I am mentally most alert, creative and productive in the mornings. So I try to do my writing, data analysis and brainstorming in the mornings, and then save meetings and lab work for the late afternoon and evenings. Everyone likely has times of the day where they are more productive at different types of tasks.

Try to find out when you are most productive with different types of tasks, and then schedule your work day and free time accordingly.

4. INCORPORATE PRODUCTIVE HOBBIES and ACHIEVE YOUR LIFE GOALS

Since I tend to feel guilty unless I feel that I am being productive- (a feeling that I think many academics share) -I have gained an affinity for hobbies that make me feel productive and achieve life goals I have outside of work.

If you feel ‘productive’ when you are doing things outside of work.. chances are that you will decrease that guilty voice in the back of your head that keeps reminding you about ‘work’. Note that your individual definition of ‘productive’ may vary from mine or someone else’s .

For instance, my mind (aka the guilty conscious) rewards me for several categories: 1) exercise/staying ninja-fit, 2) cooking up awesome meals for friends and family, 3) spending time and staying in touch with friends/family, 4) learning (including improving upon a new skill/language) 5) producing a product (artwork counts), 6) getting enough sleep, and 7) having enough alone time.

If you ‘feed your productivity meter’.. you can actually have fun and put that ‘I should be working” thought to rest. Again – being productive can include going for a swim or rollerblading (exercise points!), creating a new art piece (you needed to make something for mother’s day anyhow!), cooking with a friend (after all you need to eat -don’t you?), exercising with a friend, learning a new language (e.g. practicing spanish for that upcoming Cuba trip!), learning how to flip off of a wall, or learning a new aerial silks or capoeira move, or becoming a *certified personal fitness trainer.

*I became a NASM certified personal trainer after graduating with my PhD since I was concerned about back-up plans if I didn’t get my current postdoc…so now I have a constant plan B to make ends meet for those academic transitional periods (check out my hardly-ever updated fitness blog here, or my 10 min ab video here).

There are of course a couple of hobbies that you might have to tinker with in order to ease your guilty conscious– I admit- it’s still hard for me to curl up with a good fiction book… I’m not perfect. There is that thought in the back of my head that says ‘If you are going to be spending time reading-you should be learning something’. So instead- I curl up with a National Geographic issue or a good non-fiction book (I love Mary Roach’s books!)- since those are both relaxing and ‘productive’, thereby putting my mind at ease.

5. PLAN ACTIVITIES

My main balance tactic is to plan fun activities, with friends and family and for most of these activities to revolve around some form of physical activity (that way you have fun, socialize and exercise at the same time!).

IF you plan something, then it is easier to turn off the ‘I have to do work’ part of your mind since you already scheduled the non-work activity.

If I don’t plan something, my default for the weekend tends to be work and exercise (currently working on a 10 year streak of not missing a day of exercise…).I’ve learned from this personality disorder (blame it on my PhD!) and I try to plan at least one thing with my husband or friends every weekend so that I don’t just work away my weekend.

Some of my favorite activities to do with friends/family include: hiking/backpacking, capoeira (Afro-Brazilian martial arts), aerial silks, and surfing- all great workouts also!

For example, one of my best friends (shown below in the photo) is my former lab manager during my PhD program and we did a duo aerial silks performance together a couple years ago. We would meet at the gym, train together and have fun, and then go out to eat or cook together after. Here is our show we did a couple years back, we performed for both the Athletic Playground and for Tourettes without Regrets: Aerial Silks Show Duo

Me and Cristina performing our Aerial Duo

And with my husband- we push each other to be our better selves (mentally, physically, spiritually, etc.). Some of our favorite activities together revolve around exercise- whether it be backpacking (see picture below of us climbing half dome), capoeira, or trying out for American Ninja Warrior.

Gerid_Julie_yosemite In the end we both got on American Ninja Warrior back in 2011 and 2012 when I was doing my PhD. Here is one of my audition clips that my husband helped me make: ANW 2011 audition and here is my actual run on the obstacle course: American Ninja Warrior 2012 Venice Beach, CA

6. SET A STRUCTURED WORK-SCHEDULE AND WEEKLY ROUTINE

*Disclaimer: I have not yet conquered # 6 here yet…

I tend to still have an unstructured work schedule- where I start work at variable times throughout the week- sometimes as early as 9am and as late as 11am. This of course means that if I start at 11am, and bike to and from the lab that sometimes I don’t get home until 8 or 9pm. This sets me on a bad repetitive schedule where I get off work late, go to sleep late, wake up late.. and repeat the cycle.. ugh. It also means that if I take half a day off to deal with life stuff (DMV, go to a store/bank, etc)- that then I need to work on the weekend when everyone else is having fun…

I still have mixed thoughts about this #6, since a structured work routine would probably allow me to take more time off in the evenings and the weekends. However- it also means I would have to go to bed at a structured time, wake up early and start work early. So the jury is out on # 5 for now… but I have a feeling that once kids come along… # 6 is going to be key.

7. ANY OTHER TIPS FOR ACHIEVING WORK-LIFE BALANCE? FEEL FREE TO COMMENT!

And with that, I will be away for a bit on my honeymoon in Cuba! Whoop! And no I’m not going to do work while I’m on vacation. There’s no wifi where we are staying anyhow! (Side note..Yes I will end up working several weekends when I get back.. but that’s a cool price to pay!).

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