Thursday, July 23, 2015

Write MOAR!

I was *super* flattered to have a couple people come up to me and say the read my blog.

I know I typically don't comment on posts, so I should know there are people reading and not commenting, but as someone writing, it is nice to have feedback every now and then (I know, I know, be careful what you wish for).

But, I've been pretty quiet this first year here at Arizona State University. So, what's it been like? Well, I'm planning (and really going to try to make it happen) and longer post on it, but let's start with something small.

I can tell you, this first year as an Assistant Professor, blogging has been so far from my mind, except for rare times when I miss the time to sit down and write for fun.

Writing time the last year has been superseded (in no particular order) by:

Work:
1. Emails to students/department/colleagues/administration.
2. Preparing lectures.
3. Grant applications - research proposal writing, finding opportunities, re-writing.
4. All the random side documents that need to be filled out with grants (proposal intake forms, administrative forms for the funding agency, etc).
5. Recruiting/screening/training lab members.
6. Setting up the lab & troubleshooting.
7. Doing research!

Home:
1. Finding new childcare, doctors, dentists, optometrists
2. Finding a rental, then finding a home.
3. Actually seeing family.

This past year I have neglected working out, but excuse some of it because we bike in to campus/preschool and back most days (117F/47.2C is my cut-off).

It's also difficult to make friends, but in a way, the move, and all of the business of the first year, made it a little less obvious.  I am lucky to have some really good mentors/friends on campus. Knowing them, even if we don't hang out all the time (this isn't grad school anymore), has made a world of difference.

Now, back to work. I have two more early career fellowships to apply for this summer, and one bigger grant I'm hoping to get out before the Fall semester (and my new class!) starts.






Friday, July 10, 2015

#smbe15

I often watch conference hashtags go by, and while I learn a lot, I generally don't know what the actual name of the conference is.

In a few days I'll be tweeting (@mwilsonsayres) from #smbe15.

For your reference, this is the 2015 meeting of the Society for Molecular Biology and Evolution.

More about the meeting: http://smbe2015.at
More about the Society: https://www.smbe.org/smbe/
You can download both the schedule and the abstract book here.

J.J. Emerson and I are co-organizing and moderating a Symposium:
Symp17: Genomics of sex bias: Addressing questions with or without genomes
Wednesday July 15
Forum
11:15-12:45
and
14:15-15:45

Pooja Narang, a postdoc in my lab is presenting on some of our work:
Variable autosomal and X divergence estimates near and far from genes in great apes 
Wednesday July 15
Forum
15:00 (3:00pm)

I'll also be presenting a talk (on the last day of the conference, so don't leave early!):

Diversity varies across recombining and non-recombining regions of the human sex chromosomes
Thursday July 16
Ratstube
10:00am





Thursday, June 25, 2015

What are we up to?

Often people complain about research lab websites not being updated. In an effort to combat this I'm going to try to keep up on posting any presentations given by lab members, including posters and slides.


Okay, okay, it's a little late, but here are links to six posters of research from the Wilson Sayres lab were presented at the inaugural meeting of the Society for Evolutionary Medicine and Public Health in March 2015. The posters have now been uploaded to FigShare, and represent current research being conducted in the lab.


1. Using diversity to measure boundaries of the pseudoautosomal regions in human sex chromosomes

2. Modeling the contrasting Neolithic lineage expansions in Europe and Africa

3. Characterizing sex-biased gene expression in the green anole

4. Evolutionary perspective suggests candidate genes for variation in Turner Syndrome phenotype

5. Patterns of evolution across vertebrate sex determining genes

6. Parent-of-origin effects in Turner syndrome patients

Monday, June 8, 2015

Applications: the first year

There is a lot of pressure (internally - from myself and to be able to support my lab members, and externally - expectations from the department/college/institution) to secure funding for the lab. It has been 10 months since I started my position, and feel like I've been learning a lot along the way. When it comes to funding, I needed to learn many things, and still feel that there is a lot of learning to happen. This year I worked on four areas: developing research ideas, finding funding opportunities, deciding what to submit, and setting deadlines. And I wrote. A lot.

This is what a scientist looks like.
1. Developing research ideas. 
Before we talk about the opportunities and the deadlines, I wanted to take a step back, because no funding is possible without a good idea. I've been keeping a document where I put "potential project ideas." Most of them are a little zany. Some will never see the light of day, but if I start to think of something that might be a good future collaboration, and I know I can't work on it now, I add it to this document. I also have a white board where I list the current projects in the lab, the ones with the most preliminary data (and hopefully most likely to be funded). At least this way, I feel like I can get the ideas out of my head and not worry I'll forget about them. We'll come back to research ideas at the end, when I talk about deciding what to submit.

2. Finding funding opportunities.
I started out by looking around the NIH and NSF websites. That got hairy real fast. So, I took a step back, and started asking around locally about where people found announcements, and learned that there is a whole office devoted to pulling together funding announcements for all areas of research across the university (funding.asu.edu - though you have to sign in to get access). At other places there will be different levels of people who can help you find funding announcements. That said, even with this help, it takes time to read through and identify opportunities that are reasonable for me to apply to, but well worth the time. Even with internal resources like this, it is worth it, in my opinion, to periodically search for other funding opportunities that might be unique to you or your research area. For example, by listening to friends, I learned about some small grants available to support undergraduate research, that would never be listed on the main funding site because (in my opinion) they're not enough $ to warrant making the list, but can really help out a small lab.

3. Deciding what to submit.
For smaller and individual awards (e.g., 1-2 pages, undergraduate funding, etc), as long as there is interest, and someone to support, I'd say it is worth the time to apply. Securing trainee funding gives confidence to the trainees, provides support for an additional person, and small success can really keep you going, when it seems like other aspects of the funding game are stacked against you.

For larger awards (e.g., NIH R01, NSF proposals), for me, as a new PI, I don't have a ton of preliminary data, nor a slew of collaborators, so I felt like I really needed to focus on ideas that I could be really confident would go forward. For each of these largish grants, for each idea I had, I wrote up a one page of the Specific Aims (and Broader Impacts, where necessary), and then inquired with the program officer about whether it fit with their agency/group. I tended to get very prompt (at most a few days) and candid responses from the program offers. A few times, the answer was, "Can I be blunt? No, this isn't something our agency would consider funding." And honestly, I was so glad for the direct feedback! In these cases, I did not spend my time writing up a proposal. In a couple cases, I did receive positive feedback, and constructive criticism on what to adjust/change in the aims. For these, I did submit complete proposals.

I should pause here to say that I have no delusions that I'm going to be any more successful than my peers when applying to these, but I feel like at least I'm not starting out with a grant idea that is dead in the water. And that's something, right?

4. Setting deadlines.
When I started my position I made myself a table that lists four columns to help me stay focused and organized: 1) Award; 2) Deadline; 3) Amount awarded; and, 4) Notes.

The first three are pretty self-explanatory. Notes includes a link to the funding announcement if applicable, information about the PI/coPIs/trainees on the award, and general topic of the proposal. Then, I separated rows by Fall/Spring/Summer deadlines, and started propagating the table with planned or possible funding opportunities.

Below is the list of funding opportunities I applied for this year:
Blue - primarily or exclusively supports trainees
Crossed out - not awarded/invited
* - awarded
Italics - not yet submitted

Fall 2014
  • Bidstrup Undergrad Research Fellowship (Barrett Honors College)*
  • Mindlin Science Communication
  • Mindlin Undergrad Research Award (x 2 students)*
  • SOLUR program to support undergrad research at ASU (x 1 student)*
Spring 2015
  • NSF pre-proposal – IOS
  • SOLUR program to support undergrad research at ASU (x 3 students)*
  • NSF BEACON center award*
  • Arizona State University CLAS Undergraduate Summer Experience (x 1 student)*
  • NIH R01 - Feb 5 deadline
Summer 2015
  • Biodesign Institute Engaging Multi-Center Research internal seed (x 2 applications)
  • NIH R01 - June 5 deadline
  • Rosalind Franklin AGS award
  • Pew Fellowship (to be submitted for internal ASU evaluation)
  • Searle Fellowship (to be submitted for internal ASU evaluation)
  • Sloan Award (to be submitted for internal ASU evaluation)
  • Arizona Game and Fish Heritage Award (to be submitted)
So, in the grand scheme of things, as far as grants that "count," I've submitted one NSF pre-proposal (that was not invited for a full), and two NIH R01s (that I'm waiting to hear back from).

My sense is that this isn't too bad for the first year, but my internal pressure says I need to apply more, and I'll find out what my external pressure says in January at our annual evaluations. 

Tuesday, June 2, 2015

Deep breath

Wow. Two months since I've written here. That isn't to say that I haven't been writing, a lot. Just not here.

It was a good end of the semester.

I really enjoyed my first semester teaching, despite hiccups here and there (like not realizing that one version of the final exam mysteriously was missing an image, even though both versions were submitted in the same format).

Research is going well - I'll be heading to SMBE to present a talk on some new research from the lab, and Pooja Narang, a postdoctoral scholar working with me was chosen for an SMBE travel award to present new data that we've been working on together.

I've also submitted a some grants, big and small, with varying levels of success (still waiting to hear about the big one).

Overall, it's been a great first year, but nothing, nothing like a postdoc. :)

Wednesday, April 1, 2015

Something had to drop

I miss writing about science, and academia, and life. For fun. For you all. For me.

Before I started as an assistant professor several people told me to prepare, because I would be juggling lots of balls, and I would drop a ball. First, I think that is terrible advice. There are many better ways to convey the same concept than the "impending doom", "prepare for failure" attitude. 

But second, perhaps it is a little true. Between setting up the lab, finding and writing grant applications, mentoring students, writing lectures and teaching, emails (so many emails), and hoping to spend any time with the people around me, I have severely limited the time I spend writing for fun.

The posts are usually written from notes taken for some other reason.

I guess this is just check in that things are crazy busy, exciting, exhausting, and something had to drop. That something was sharing in depth here. For now.*

#newPI out


*I had a few "extra" minutes this morning because the dog got me up earlier than usual. I could have taken a short run (I do remember a time when I exercised regularly), but prioritized this. Today. Now on to answering emails.

Thursday, March 26, 2015

Congratulations to Pooja Narang for SMBE Travel award and Talk!

Dr. Pooja Narang, a postdoctoral research scientist in the Wilson Sayres lab, was selected to receive an SMBE Young Investigator Travel Award to attend the 2015 meeting of the Society for Molecular Biology and Evolution in Vienna, Austria, where she will be presenting about our new research results investigating patterns of male mutation bias. 

Congratulations!! 

Tuesday, March 17, 2015

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

I'm super excited to share our new paper, out in Advanced Access in Genome Research, A recent bottleneck of Y chromosome diversity coincides with a global change in culture!

Update: you can listen to a local NPR interview with Mark Brodie about this work here: http://kjzz.org/content/116152/does-evolution-favor-rich-and-powerful

In a nutshell:

Graphic designed by Sabine Deviche.

To help explain the paper, check out this ASUnews article by Sandra Leander: https://asunews.asu.edu/20150316-y-chromosome-bottleneck

And, for a longer, visual, explanation, check out this *awesome* infographic made for us by Sabine Deviche.

Graphic designed by Sabine Deviche.
One on the methods we use to study the Y chromosome and mtDNA is the coalescent. Here is a short video explaining the coalescent, and highlighting the difference between census population size (all the people in the population, and the effective population size (those people who left genetic relics in our DNA that we can study today):


A recent bottleneck of Y chromosome diversity coincides with a global change in culture

    • Monika Karmin*
    • Lauri Saag*
    • Mário Vicente*
    • Melissa A. Wilson Sayres*
    • Mari Järve
    • Ulvi Gerst Talas
    • Siiri Rootsi
    • Anne-Mai Ilumäe
    • Reedik Mägi
    • Mario Mitt
    • Luca Pagani
    • Tarmo Puurand
    • Zuzana Faltyskova
    • Florian Clemente
    • Alexia Cardona
    • Ene Metspalu
    • Hovhannes Sahakyan
    • Bayazit Yunusbayev
    • Georgi Hudjashov
    • Michael DeGiorgio
    • Eva-Liis Loogväli
    • Christina Eichstaedt
    • Mikk Eelmets
    • Gyaneshwer Chaubey
    • Kristiina Tambets
    • Sergei Litvinov
    • Maru Mormina
    • Yali Xue
    • Qasim Ayub
    • Grigor Zoraqi
    • Thorfinn Sand Korneliussen
    • Farida Akhatova
    • Joseph Lachance
    • Sarah Tishkoff
    • Kuvat Momynaliev
    • François-Xavier Ricaut
    • Pradiptajati Kusuma
    • Harilanto Razafindrazaka
    • Denis Pierron
    • Murray P. Cox
    • Gazi Nurun Nahar Sultana
    • Rane Willerslev
    • Craig Muller
    • Michael Westaway
    • David Lambert
    • Vedrana Skaro
    • Lejla Kovačević
    • Shahlo Turdikulova
    • Dilbar Dalimova
    • Rita Khusainova
    • Natalya Trofimova
    • Vita Akhmetova
    • Irina Khidiyatova
    • Daria V. Lichman
    • Jainagul Isakova
    • Elvira Pocheshkhova
    • Zhaxylyk Sabitov
    • Nikolay A. Barashkov
    • Pagbajabyn Nymadawa
    • Evelin Mihailov
    • Joseph Wee Tien Seng
    • Irina Evseeva
    • Andrea Bamberg Migliano
    • Syafiq Abdullah
    • George Andriadze
    • Dragan Primorac
    • Lubov Atramentova
    • Olga Utevska
    • Levon Yepiskoposyan
    • Damir Marjanović
    • Alena Kushniarevich
    • Doron M. Behar
    • Christian Gilissen
    • Lisenka Vissers
    • Joris A. Veltman
    • Elena Balanovska
    • Miroslava Derenko
    • Boris Malyarchuk
    • Andres Metspalu
    • Sardana Fedorova
    • Anders Eriksson
    • Andrea Manica
    • Fernando L. Mendez
    • Tatiana M. Karafet
    • Krishna R. Veeramah
    • Neil Bradman
    • Michael F. Hammer
    • Ludmila P. Osipova
    • Oleg Balanovsky
    • Elza K. Khusnutdinova
    • Knut Johnsen
    • Maido Remm
    • Mark G. Thomas
    • Chris Tyler-Smith
    • Peter A. Underhill
    • Eske Willerslev
    • Rasmus Nielsen
    • Mait Metspalu*
    • Richard Villems*
    • and Toomas Kivisild*

  1. 1Estonian Biocentre, Tartu, 51010, Estonia;
  2. 2Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
  3. 3Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51010, Estonia;
  4. 4Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom;
  5. 5Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA;
  6. 6School of Life Sciences and The Biodesign Institute, Tempe, Arizona, USA;
  7. 7Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
  8. 8Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia;
  9. 9Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
  10. 10Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia;
  11. 11Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, Russia;
  12. 12Department of Psychology, University of Auckland, Auckland, 1142, New Zealand;
  13. 13Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA;
  14. 14Department of Applied Social Sciences, University of Winchester, Winchester, United Kingdom;
  15. 15The Wellcome Trust Sanger Institute, Hinxton, United Kingdom;
  16. 16Center of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics and Gynecology, Tirana, Albania;
  17. 17Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark;
  18. 18Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia;
  19. 19Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia;
  20. 20Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
  21. 21School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA;
  22. 22Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
  23. 23DNcode Laboratories, Moscow, Russia;
  24. 24Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France;
  25. 25Eijkman Institute for Molecular Biology, Jakarta, Indonesia;
  26. 26Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand;
  27. 27Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka, Bangladesh;
  28. 28Arctic Research Centre, Aarhus University, Aarhus, DK-8000, Denmark;
  29. 29Environmental Futures Research Institute, Griffith University, Nathan, Australia;
  30. 30Genos, DNA Laboratory, Zagreb, Croatia;
  31. 31University of Osijek, Medical School, Osijek, Croatia;
  32. 32Centogene AG, Rostock, Germany;
  33. 33Institute of Bioorganic Chemistry, Academy of Science, Tashkent, 100143, Uzbekistan;
  34. 34Institute of Cytology and Genetics, Novosibirsk, Russia;
  35. 35Institute of Molecular Biology and Medicine, Bishkek, Kyrgyzstan;
  36. 36Kuban State Medical University, Krasnodar, Russia;
  37. 37L. N. Gumilyov Eurasian National University, Astana, Kazakhstan;
  38. 38Center for Life Sciences, Nazarbayev University, Astana, Kazakhstan;
  39. 39Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russia;
  40. 40Laboratory of Molecular Biology, Institute of Natural Sciences, M. K. Ammosov North-Eastern Federal University, Yakutsk, Russia;
  41. 41Mongolian Academy of Medical Sciences, Ulaanbaatar, Mongolia;
  42. 42National Cancer Centre Singapore, Singapore;
  43. 43Northern State Medical University, Arkhangelsk, Russia;
  44. 44Anthony Nolan, London, UK;
  45. 45Department of Anthropology, University College London, London, United Kingdom;
  46. 46RIPAS Hospital, Bandar Seri Begawan, Brunei;
  47. 47Scientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Tbilisi, Georgia;
  48. 48St. Catherine Specialty Hospital, Zabok, Croatia;
  49. 49Eberly College of Science, Pennsylvania State University, University Park, Pennsylvania, USA;
  50. 50University of Split, Medical School, Split, Croatia;
  51. 51V. N. Karazin Kharkiv National University, Kharkiv, Ukraine;
  52. 52Department of Genetics and Bioengineering, Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, Bosnia and Herzegovina;
  53. 53Institute of Genetics and Cytology, National Academy of Sciences, Minsk, Belarus;
  54. 54Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands;
  55. 55Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, Russia;
  56. 56Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia;
  57. 57Department of Zoology, University of Cambridge, Cambridge, United Kingdom;
  58. 58Integrative Systems Biology Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia;
  59. 59Department of Genetics, Stanford University School of Medicine, Stanford, California, USA;
  60. 60ARL Division of Biotechnology, University of Arizona, Tucson, Arizona, USA;
  61. 61Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA;
  62. 62The Henry Stewart Group, London, United Kingdom;
  63. 63Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia;
  64. 64University Hospital of North Norway, Tromsøe, Norway;
  65. 65Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom;
  66. 66Estonian Academy of Sciences, Tallinn, Estonia
  1. Corresponding authors: tk331@cam.ac.ukmonika.karmin@gmail.com
  1. * These authors contributed equally to this work.

Abstract

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.


-------------------------------------
Update: Popular Science articles about this research:

Francie Diep, science journalist, Pacific Stand
http://www.psmag.com/nature-and-technology/17-to-1-reproductive-success

Danielle Paquette, Washington Post
http://www.washingtonpost.com/blogs/wonkblog/wp/2015/03/18/how-wealth-trumped-natural-selection-and-changed-our-ancestors-sex-lives/?hpid=z4

Mark Brodie, KJZZ, NPR radio
http://kjzz.org/content/116152/does-evolution-favor-rich-and-powerful

Estonian paper
http://pluss.postimees.ee/3131333/geenid-naitavad-urgmeeste-voimu

Amanda Marcotte, Slate:
http://www.slate.com/blogs/xx_factor/2015/03/20/the_brutality_of_the_stone_age_only_1_man_had_children_for_every_17_women.html?wpsrc=fol_fb

Janet Feng, IFLS
http://www.iflscience.com/health-and-medicine/women-were-out-reproducing-men-4000-years-ago

reddit
http://www.reddit.com/r/science/comments/2zcudp/wealth_and_power_may_have_played_a_stronger_role/

Genetic Engineering and Biotechnology News
http://www.genengnews.com/gen-news-highlights/male-genes-preserve-survival-of-the-wealthiest-legacy/81251045/

Sarah Kaplan, Washington Post
http://www.washingtonpost.com/news/morning-mix/wp/2015/03/18/how-survival-of-the-fittest-became-survival-of-the-richest/

IANS, The Economic Times
http://economictimes.indiatimes.com/magazines/panache/wealth-behind-decline-in-number-of-reproducing-males-study/articleshow/46609782.cms

Will Parker, Science GoGo
http://www.scienceagogo.com/news/20150216195902.shtml

ANI, ZeeNewsIndia
http://zeenews.india.com/news/sci-tech/male-genetic-diversity-declined-due-to-wealth-power-rather-than-survival-of-fittest_1563084.html

News Staff, Science2.0
http://www.science20.com/news_articles/social_fitness_did_a_genetic_bottleneck_occur_because_of_wealth_and_power-154047

Anthony Rivas, Medical Daily
http://www.medicaldaily.com/did-cultural-shift-influence-human-evolution-how-farming-might-have-changed-genetic-326094