Journal Club

We meet weekly on Fridays to discuss articles within the broad area of evolutionary genetics, including but not limited to population genomics. Occasionally we also have our journal club at the Gamla Orangeriet, in the Botanical Garden. Below you can find the papers we will be reading and discussing.

lab_jc_coffee

Journal club and cake at Gamla Orangeriet

 

June 8th: Silencing of virulence genes by plant small RNAs in extracellular vesicles

Jörg will present a new paper in Science by Cai et al, entitled “Plants send small RNAs in extracellular vesicles to fungal pathogen to silence virulence genes”. We will meet at DEEP in N340 at 14:30.

June 1st: Plant mating system variation

Ben will present a review paper on mating system variation among populations, across a broad range of plant species.

Whitehead, M. R., Lanfear, R., Mitchell, R. J., & Karron, J. D. (2018). Plant Mating Systems Often Vary Widely Among PopulationsFrontiers in Ecology and Evolution6, 38.

Note, at 1 pm!

May 25th: Recent literature round-up

We will meet in room N391 at DEEP – everyone brings two recent papers that would be interesting to discuss. Note, at 1 pm!

April 6th: Gene birth on the Y chromosome

Verena will present this study of the rate of gene transfer to the Drosophila Y chromosome. We meet at 14:30 in N340 at DEEP.

March 23rd: The tempo of evolutionary decline in self-compatible plant lineages

Jörg will present this bioRxiv preprint on the evolutionary decline in self-compatible plants. We meet at 14:30 in N340 at DEEP.

March 16th: Non-bifurcating history of species from the Arabidopsis genus

We will discuss this paper by Novikova and colleagues on the complex history of species from the genus Arabidopsis. Presenter: Robert. Room: TBA, but at DEEP, 14:30.

March 8th: More machine learning for population genetics

We will discuss an example of machine learning for detecting different types of sweeps.

Schrider DR, Kern A. 2016. S/HIC: Robust identification of soft and hard sweeps using machine learning. PLoS Genetics doi: 10.1371/journal.pgen.1005928 

Note! We will meet on Thursday March 8th, at 2 pm at SciLifeLab (room Becquerel, gamma 5).

February 23rd: Machine learning for population genetics

Ben will present a recent review in Trends in Genetics on supervised machine learning for population genetics by Schrider and Kern. We meet at 14:30 in room N340, at DEEP.

February 9th: Loss of self-incompatibility in A. thaliana

Tanja will present a nice example of a study demonstrating the genetic basis of loss of SI in A. thalianaTsuchimatsu 2010. Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene. Nature 464: 1342-1346. We meet at 14:30 in room N491, at DEEP.

February 2nd: Range expansion and adaptive evolution

Marco will present a paper by González-Martinez et al. 2017 on the impact of selection in different parts of the range of an outcrossing plant. Also see this related paper (with some familiar co-authors!). We meet at 3:00 pm, DEEP room N340.

January 26th: A soft sweep in Africanized honeybees

Xuyue will present a recent paper by Avalos et al. (2017) in Nature Communications on a soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee. We meet at 2:30 pm, DEEP room N340.

January 19th: Open JC

Everyone brings 2-3 papers that they think would be interesting to discuss – please be prepared to tell the others why you think the papers you chose are interesting. We will meet at 2.30 pm, DEEP room N340. There may be cake…

December 8th: Evolution of flower colour pattern in snapdragons

Robert will present this paper by Bradley et al. (2017) on the role of regulatory small RNAs for flower colour pattern in a snapdragon hybrid zone.

November 24th: Origin and evolution of a young Y chromosome in Asparagus

Tanja will present this paper by Harkess et al. (2017) on the origin and evolution of a young Y chromosome in Asparagus officinalis.

November 17th: The unusual S-locus of Leavenworthia

Ben will present this paper on the unusually structured S-locus of Leavenworthia:

Chantha, S. C., Herman, A. C., Castric, V., Vekemans, X., Marande, W., & Schoen, D. J. (2017). The unusual S locus of Leavenworthia is composed of two sets of paralogous loci. New Phytologist 216: 1247-1255. At DEEP, N340, 14.00.

November 8th: Genetic variation for pseudo-self-compatibility in Leavenworthia

Marco will present a paper by Baldwin and Schoen on genetic variation for pseudo-self-compatibility in Leavenworthia alabamica. Note on Wednesday at DEEP, N340, 14.00.

October 26th: Selection in asexual mites

Jörg will present a recent paper by Brandt et al. 2017. Effective purifying selection in ancient oribatid mites. Nature Communications 8:873. Note on Thursday at DEEP, N340, 13.00.

October 20th: Gene expression drives the evolution of dominance

This Friday we will discuss a preprint by Huber et al. where the authors utilize mating system differences between Arabidopsis species to estimate dominance effects of new amino acid changing mutations from genomic data. Presenter: Tanja, Location: DEEP, N340.

October 13th: Recent literature round-up JC

Everyone picks 2 recent papers of interest and prepares to tell the others why they chose them/what they found interesting. We meet at DEEP (room N340) at 1 pm. Cake at Gamla Orangeriet afterwards!

September 14th: Early history and transition to selfing in Arabidopsis thaliana

Jörg will lead the discussion of this recent paper by Durvasula and colleagues: Durvasula et al. 2017. African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. PNAS 114: 5214-5218

April 28th: Supergene evolution

We will discuss a recent paper on the genetic architecture of the Primula S-locus supergene: Li et al. 2016. Nature Plants.

Location: N340, DEEP N340, Stockholm University

Presenter: Jörg

April 7th: Selection on reproductive genes in plants

We will discuss an MBE paper from 2013 by Arunkumar et al. on the impact of selection on genes expressed in pollen in Capsella grandiflora.

Location: N491, DEEP, Stockholm University

Presenter: Juanita

March 10th: Serial founder events and mutational load

We will discuss a recent paper in PNAS by Henn et al. on the impact of serial bottlenecks on genetic load in human populations.

Location: N491, DEEP, Stockholm University.

Presenter: Ben

February 24th: The effect of an extreme and prolonged bottleneck on patterns of deleterious variation

We will discuss a recent paper in Genetics where Pedersen et al. combine analyses of population genomic data with simulations, to characterise the effects of a long and severe bottleneck on deleterious variation and evaluate different measures of genetic load. Location: N491, DEEP, Stockholm University.

Presenter: Tanja

February 9th: Transposable elements and gene regulation

We will discuss a recent paper in eLife entitled “Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation” by Stuart et all, on Friday at 2.30 pm at Gamla orangeriet.

Presenter: Robert

January 25th: Origin of the allotetraploid Arabidopsis suecica

We will discuss a recent paper in MBE entitled “Genome sequencing reveals the origin of the allotetraploid Arabidopsis suecica” by Novikova et al., on Thursday at 1 pm at SciLifeLab (Hertz, Gamma 6).

Presenter: Andy

August 19th: Recent literature JC

Everyone picks 2-3 recent papers of interest and summarizes them. This time we will meet at 1 pm at Gamla Orangeriet.

Here is the list of papers we discussed.

June 10th: Ancient DNA from sediments

Engy will present this review paper on ancient DNA from sediments and their impact on reconstruction of past biodiversity.

Birks et al. 2016. How have studies of ancient DNA from sediments contributed to the reconstruction of Quaternary floras? New Phytologist 209: 499-506

June 2nd: Regions of open chromatin are enriched for variants with effects on gene expression and phenotypic trait variation in maize

Rodgers-Melnick E, Vera DL, Bass HW and Buckler ES 2016. Open chromatin reveals the functional maize genome. Proceedings of the National Academy of Sciences:201525244

Presenter: Robert. Note: On Thursday, at SU.

May 27th: Detecting balancing selection

Jörg will present this review paper on the limits and prospects for detecting balancing selection in genomes. Note that we will start at 3 pm!

Fijarczyk and Babik. 2015. Detecting balancing selection in genomes: limits and prospects. Molecular Ecology 24: 3529-45.

May 20th: Recent selection for self-compatibility in Leavenworthia

This week we will read a recent paper on population genetic patterns surrounding the S-locus in a self-compabtible population of Leavenworthia alabamica:

Herman AC and Schoen DJ. Recent selection for self-compatibility in a population of Leavenworthia alabamica. Evolution Advance Access doi: 10.1111/evo.12937

Presenter: Andy

May 13th: Genomic distribution of conserved noncoding elements and association with gene expression in mammals

Babarinde & Saitou 2016 MBE Genomic locations of conserved noncoding sequences and their proximal protein-coding genes in mammalian expression dynamics

Presenter: Kim

April 29th: Linked selection and demographic inference

Schrider D, Shanku AG, Kern AD. 2016. Effects of linked selective sweeps on demographic inference and model selection. bioRxiv Presenter: Tanja

Cornille A, Salcedo A, Kryvokhyzha D, Glémin S, Holm K, Wright S, Lascoux M. 2016. Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd’s purse (Capsella bursa‐pastoris). Molecular Ecology 25:616-629. Presenter: Ben

Note: We will meet at the Gamla Orangeriet this week.

April 8th: First recent literature JC

Everyone picks 3-5 recent papers of interest and summarizes them. Here is the list of papers and links that we discussed.

Note: We will meet at the Gamla Orangeriet this week.

April 1st: Linked selection and Lewontin’s paradox

Ben will present this commentary: Coop G. 2016. Does linked selection explain the narrow range of genetic diversity across species? BioRxiv doi: http://dx.doi.org/10.1101/042598

March 18th: Sex speeds adaptation by altering the dynamics of molecular evolution

McDonald MJ, Rice PJ, Desai MM. 2016. Sex speeds adaptation by altering the dynamics of molecular evolution. Nature doi:10.1038/nature17143

Presenter: Jörg

March 11th: Evolution of DNA methylation

Ben and Kim will present this short review paper on DNA methylation: Zhong. 2016. Comparative epigenomics: a powerful tool to understand the evolution of DNA methylation. New Phytologist 210:76-80

February 17th:  The complications of inferring relaxed purifying selection in non equilibrium situations. NB change of time: Friday at 10.30 am!

Tanja will present this short review paper: Brandvain and  Wright. 2016. The limits of natural selection in a nonequilibrium world. Trends in Genetics, in press.

February 12th: Cis-regulatory evolution

Kim will present this paper on cis-regulatory evolution: Fyon et al. 2015. Enhancer runaway and the evolution of diploid gene expression. PLoS Genetics 11(11): e1005665

November 20th: Evolution and silencing of repeats in Arabidopsis and relatives

We will read and discuss this paper on the age distribution and silencing of repeats in the Arabidopsis thaliana genome: Maumus F, Quesneville H. 2014. Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana. Nat Commun 5:4104.

Presenter: Tanja

This paper is also relevant for those going to Brandon Gaut’s seminar at EBC in Uppsala on Tuesday November 17th at 14.00 (Lindahlsalen).

November 12th (NOTE, Thursday, at SciLifeLab!): Organizing computational biology projects

We will read and discuss organization of genomics projects, based on this paper in PLoS Computational Biology: Stafford Noble 2009. A quick guide to organising computational biology projects. PLoS Computational Biology 5(7): e1000424.

November 6th: Evolution of dominance at the Brassicaceae self-incompatibility locus

Durand et al. 2014. Dominance hierarchy arising from the evolution of a complex small RNA regulatory network. Science 346:1200–1205.

October 30th: Dissecting the genetic basis of a complex cis-regulatory adaptation

Naranjo et al 2015 bioRxiv Dissecting the genetic basis of a complex cis-regulatory adaptation
http://biorxiv.org/content/early/2015/10/15/029207
Presenter: Kim

October 23rd: Widespread genomic signatures of natural selection in hominid evolution

McVicker et al. 2009. PLoS Genetics 5: e1000471 Presenter: Ben

October 8th: Detecting recent selective sweeps in the presence of background selection and varying mutation rate

NOTE! On THURSDAY, at SciLifeLab, gamma 6, before lunch.

Huber CD, DeGiorgio M, Hellman I, Nielsen R. Molecular Ecology. 2015.  doi: 10.111/mec. 13351 Presenter: Ben

September 26th: Interaction between gene expression and purifying selection in maize

Dilip Pophaly S, Tellier A. 2015. Population level purifying selection and gene expression shape sub genome evolution in maize. Molecular Biology and Evolution, in press. Presenter: Kim

September 17th: Frequent adaptation and the McDonald-Kreitman test

NB! On THURSDAY, at SciLifeLab, gamma 6.

We will discuss this paper on the impact of linked selection on analyses based on extensions of the classic McDonald-Kreitman test.

Messer PW, Petrov DA. 2013. Frequent adaptation and the McDonald-Kreitman test. PNAS 110:8615-8620 Presenter: Tanja

September 11th: Allopolyploidy and gene expression evolution

We will discuss this paper which deals with genetic and epigenetic mechanisms for gene expression changes in polyploids:

Shi et al. 2015. Genome-Wide Dosage-Dependent and -Independent Regulation Contributes to Gene Expression and Evolutionary Novelty in Plant Polyploids. Molecular Biology and Evolution 32: 2351-2366. Presenter: Kim

September 4th: Mating systems and molecular evolution

For this session, we will discuss a recent paper on patterns of molecular evolution and efficacy of natural selection in outcrossing and selfing snails: Burgarella et al. 2015. Molecular Evolution of Freshwater Snails with Contrasting Mating Systems. Molecular Biology and Evolution, 32:2403–2416 Presenter: Ben

August 28th, 2015: Heterozygosity and mutation rates – a feed-forward loop?

We will discuss Yang et al. 2015. Parent-progeny sequencing indicates higher mutation rates in heterozygotes. Nature 523: 463-467. Presenter: Tanja

For background reading, see Tian et al. 2008. Nature 455: 105-108, and this nice perspective piece written by Michael Lynch.