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. 


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:

In a nutshell:

Graphic designed by Sabine Deviche.

To help explain the paper, check out this ASUnews article by Sandra Leander:

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:
  1. * These authors contributed equally to this work.


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

Danielle Paquette, Washington Post

Mark Brodie, KJZZ, NPR radio

Estonian paper

Amanda Marcotte, Slate:

Janet Feng, IFLS


Genetic Engineering and Biotechnology News

Sarah Kaplan, Washington Post

IANS, The Economic Times

Will Parker, Science GoGo

ANI, ZeeNewsIndia

News Staff, Science2.0

Anthony Rivas, Medical Daily