lab_meeting
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Summer 2021

3-4 pm each Tuesday via Zoom or outdoors

July 27 Botany meeting recap. Last lab meeting of the summer

July 8 3-4 pm Botany practise talks

Erin poster

Alex poster

Zack poster

July 7 3-4 pm Botany practise talks

Rebekah 12-min talk

Aaron 12-min talk

Jun 22 Campus ice cream shop and each lab member share a paper

Jun 15 Optional lab trip to the Quaking Bog, Theodore Wirth Park to check on a local natural population of Drosera rotundifolia

Jun 1 Share papers, summer SMART goals

Previous semesters

Spring 2021

Via zoom 2-3 pm on Fridays.

Apr 30 Lab trip to Theodore Wirth park

Apr 16 Marian Schubert

Mar 26 Discuss work from seminar speaker Kenji Fukushima

Mar 13 Diego on parametric bootstrap and coalescence simulation

https://academic.oup.com/sysbio/article/61/1/44/1679302 

Mar 6 Lab get-together at Como Park

Feb 19 Diego on detecting hybridization and introgression

Review paper https://ecoevorxiv.org/uahd8/

Feb 5 Diego on analyzing gene tree discordance

PhyParts https://bmcecolevol.biomedcentral.com/articles/10.1186/s12862-015-0423-0

Quartet Sampling https://pubmed.ncbi.nlm.nih.gov/29746719/ 

Jan 22 Lab member updates and SMART goals

Coordinate onsite work (office, lab, sunrise application)

Fall 2020

Via zoom 2-3 pm on Fridays

Dec 11 Zack intro and lab end-of-the year photo share

Nov 13 Diego on Amaranthaceae gene tree analyses and side projects

Oct 23 Ya

Multiple Genetic Trajectories to Extreme Abiotic Stress Adaptation in Arctic Brassicaceae

https://academic.oup.com/mbe/article/37/7/2052/5804990

Oct 9 Lab trip to Taylors Falls

Sep 25 joint lab meeting with Matt Johnson’s Lab

Sep 18 Aaron Lee on undergrad work

Summer 2020

Via zoom 1pm every other Fridays

Jul 10 Botany practise talk round 2: Nan, Diego, and Alex

July 3 Botany practise talk round 1: Rebekah and Ya

Jun 12 Rebekah

Genomes of the Venus Flytrap and Close Relatives Unveil the Roots of Plant Carnivory

https://doi.org/10.1016/j.cub.2020.04.051

May 29 Diego

The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales

https://doi.org/10.1101/2020.05.26.112318

Spring 2020

Via zoom 1pm weekly on Fridays

May 8 Postdoc job candidate presentation

Apr 24 Alex preliminary anthocyanin gene analysis

Caryophyllales NSF proposal as background reading

Apr 17 Rebekah Drosera chromosome number MS draft

Drosera NSF proposal as background reading.

Apr 10 Diego Hyb-Seq MS draft

Apr 3 Ya

Phylogenetics is the New Genetics (for Most of Biodiversity) https://doi.org/10.1016/j.tree.2020.01.005

Mar 27 Nan

A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

https://doi.org/10.3389/fgene.2019.01407 Background, terminology, and considerations

Fall 2019

4–5 pm in 712 BioSci every other week

Nov 11 2pm (Diego away)

Rebekah practise talk.

Oct 31 Rebekah

Interaction among ploidy, breeding system and lineage diversification

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.16184 

Oct 17 Nan Ph.D. project

Oct 3 Diego and Ya

A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens

https://www.frontiersin.org/articles/10.3389/fpls.2019.00937/full

https://www.frontiersin.org/articles/10.3389/fpls.2019.01102/full

Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms

Sep 19 Diego

Factors Influencing Gene Family Size Variation Among Related Species in a Plant Family, Solanaceae

https://academic.oup.com/gbe/article/10/10/2596/5100825#122164049

Sep 5 Lunch together welcome Alex and welcome back!

Summer 2019

4–5 pm in 712 BioSci every other week

Aug 13 Joint meeting with PROST

Signatures of Microevolutionary Processes in Phylogenetic Patterns

https://academic.oup.com/sysbio/article/68/1/131/5043295

Aug 8 Diego recap on Botany meeting

Hybridization and diversification are positively correlated across vascular plant families

https://www.biorxiv.org/content/10.1101/724377v2

July 25 Alex presentation on her Master’s thesis research

July 11 A closer look at the 353 kit

A phylogenomic analysis of Nepenthes (Nepenthaceae)

https://www.biorxiv.org/content/10.1101/680488v1.full

We need to optimize our own baits: long exon, higher hybrid efficiency, our own genes of targetNew pipeline for bait design that include genomes - Botany poster

Spring 2019

Lab meetings on hold as Ya is teaching and Chen is away

Jan 17 Rebekah practise lightening talk for Bell Advisory Board meeting

Fall 2018

Dec 14 Chen

Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution

https://www.annualreviews.org/doi/abs/10.1146/annurev-cellbio-100913-012908 

Dec 7 Rebekah

OrthoFinder2: fast and accurate phylogenomic orthology analysis from gene sequences

https://www.biorxiv.org/content/early/2018/11/08/466201 

Nov 30 Chapter 7 and 8 of Harmon book Sep 14 Chapter 6 of Harmon book https://lukejharmon.github.io/pcm/chapters/ 

Oct 26 to Nov 16 No lab meeting due to people traveling

Oct 22 Delphine and Diego

A maximum pseudo-likelihood approach for phylogenetic networks

https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-16-S10-S10

Oct 19 Lab trip to Taylor Falls

Oct 12 Ya

Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics https://academic.oup.com/mbe/article/31/11/3081/2925722 

Oct 5 Delphine introducing her work on C2 physiology and goal for her visit

Sep 28 Chen project update

Sep 21 No lab meeting. Diego and Ya in Mexico

Sep 14 Chapter 6 of Harmon book https://lukejharmon.github.io/pcm/chapter6_beyondbm/ 

Sep 7 Chapter 5 of Harmon book https://lukejharmon.github.io/pcm/chapter5_mvbm/Difference between correlation vs. regression

Summer 2018

Aug 24 Rebekah Fulbright proposal

Aug 22 Diego ABBA-BABA test

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

https://academic.oup.com/sysbio/article/64/4/651/1650669 

Great discussion on the promise and limitations of using ABBA-BABA test for detecting introgression.

Aug 17 Diego hybridization

Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes https://www.nature.com/articles/s41467-018-05479-9

Aug 10 Chen

Phylogenomic Mining of the Mints Reveals Multiple Mechanisms Contributing to the Evolution of Chemical Diversity in Lamiaceae https://www.sciencedirect.com/science/article/pii/S1674205218301898

Jul 20 Botany practice talk

May 30 SSB practise talk: Chen and Diego

May 25 Chain of Lakes Lab Trip

May 18 Chen benchmark paper figure review

May 11 Chapter 4 of Harmon’s Comparative methods book https://lukejharmon.github.io/pcm/chapter4_fitbm/

And the 1985 PIC paper: Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat. 125:1–15.

We went through the math but couldn’t figure out the branch extension bit form either the Harmon book or the 1985 PIC paper

Spring 2018

2018-4-20 Chapter 3 of Harmon’s comparative methods book

https://lukejharmon.github.io/pcm/chapters/ 

2018-4-13 Diego

Chapter 1 and 2 from Luke’s book https://lukejharmon.github.io/pcm/chapter1_introduction/ 

We loved the book. Flipping lizards makes a lot of sense!

2018-4-6 Chen

A new method for decontamination of de novo transcriptomes using a hierarchical clustering algorithm. https://www.ncbi.nlm.nih.gov/pubmed/28011783

Doesn’t seem that helpful..

2018-3-30 Rebekah

Stochastic Mapping of Morphological Characters

http://www.nielsenlab.org/wp-content/uploads/2011/07/Huelsenbeck-J.-P.-Syst.-Biol.-2003.pdf 

2018-3-9 Rebekah project methods in niche analysis

Combining Historical Biogeography with Niche Modeling in the Caprifolium Clade of Lonicera (Caprifoliaceae, Dipsacales) https://academic.oup.com/sysbio/article/59/3/322/1703086

2018-3-2 Ya Co-expression network + phylogenomics in non-model species

Shifts in gene expression profiles are associated with weak and strong Crassulacean acid metabolism http://onlinelibrary.wiley.com/doi/10.1002/ajb2.1017/full 

2018-2-14 Rebekah lead a discussion of Ch 2 in the book

Carnivorous Plants: Physiology, ecology, and evolution

2018-2-7 Chen share ideas on his DGE benchmark project

Fall 2017

2017-11-12 Diego

IsoSel: Protein Isoform Selector for phylogenetic reconstructions

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0174250

2017-11-10 Chen

Read mapping softwares

Problem with low % uniquely mapped in polyploids?

2017-11-8 Diego & Chen

Papers on synteny-informed homology inference. Essentially one method but these papers cite previous paper for calculating scores:

GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm

(the benchmark paper)

https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-016-0684-2 

Quantitative synteny scoring improves homology inference and partitioning of gene families

(the paper introducing modified algorithm)

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S15-S12

Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins

(The original algorithm paper)

http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000063&type=printable 

2017-11-3 Chen

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

http://www.nature.com/nbt/journal/v33/n3/full/nbt.3122.html 

https://ccb.jhu.edu/software/stringtie/ 

2017-11-1 Diego

Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses https://www.nature.com/articles/s41598-017-13236-z

2017-10-25 Ya

A critical comparison of technologies for a plant genome sequencing project

https://www.biorxiv.org/content/early/2017/10/11/201830?rss=1 

2017-9-26 Chen

WGCNA: an R package for weighted correlation network analysis

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-559

2017-9-25 Rebekah

Gene ontology

Annotated genes and non-annotated genomes: cross-species use of Gene Ontology in ecology and evolution research

Primmer et al. 2013 Molecular Ecology

http://onlinelibrary.wiley.com/doi/10.1111/mec.12309/full 

Summer 2017

2017-8 Chen

OrthoFinder, OrthoMCL, vs. other orthology inference methods

2017-5-10 Chen

Wisecaver et al. 2017 Plant Cell

A Global Co-expression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants

http://www.plantcell.org/content/early/2017/04/13/tpc.17.00009.abstract 

Lab meeting ideas:

How to organize/backup data and code: Jpyter, Git, markdown file

An idea for a project – A literature review – A single paper – Problematic data, confusing findings – Analyses that didn’t work – Analyses that worked – A tutorial on a technique they mastered – Something they learned in class – A paper outline

Small useful unix tools such as awk and screen

Choose a book or two from below:

The Theory of Evolution: Principles, Concepts, and Assumptions

Edited by Scheiner, Samuel M ; Mindell, David P

Chicago: University of Chicago Press 2020

You can access the ebook from the umn library

The Role of Mathematics in Evolutionary Theory

Otsuka, Jun

University of Cambridge Press, 2019

You can access the ebook from the umn library. Written by a philosopher.

Caryophyllales: Evolution and Systematics

Edited by H.-D. Behnke and T.J. Mabry

Great summary of old/classic literature on Caryophyllales from the pre-molecular phylogeny era, when people actually cared about chemistry, cytology, anatomy, and many other cool aspects. PDF: https://drive.google.com/drive/folders/1yzY9KdxbFIqX9ZTWFkrX6psLjrc18jVp 

Molecular Evolution: a statistical approach

By Ziheng Yang, 2014

Quite math-heavy and dry.

Computational Phylogenetics: An Introduction to Designing Methods for Phylogeny Estimation

by Tandy Warnow, 2017

A bit difficult to follow and assumes some comp sci background

Papers for the future (feel free to add)

Wong et al. 1kp review 

Molecular rate and selection Ch 4.4, 4.5, and 4.6 of “Phylogenetics in the Genomic Era”

ASPEN, a methodology for reconstructing protein evolution with improved accuracy using ensemble models https://elifesciences.org/articles/47676

A divide-and-conquer method for building large gene family trees

https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-020-00789-1

Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution

Related to Nan’s work

https://academic.oup.com/mbe/article/34/10/2690/4010934

The Influence of Polyploidy on the Evolution of Yeast Grown in a Sub-Optimal Carbon Source

Inference of Ancient Whole-Genome Duplications and the Evolution of Gene Duplication and Loss Rates https://academic.oup.com/mbe/article/36/7/1384/5475503

Machine learning for phylogeny

https://www.biorxiv.org/content/biorxiv/early/2019/10/05/781252.full.pdf

https://www.biorxiv.org/content/10.1101/787168v1

Genome scan of Fst for introgression https://www.biorxiv.org/content/biorxiv/early/2019/09/28/752758.full.pdf?%3Fcollection=

https://www.biorxiv.org/content/biorxiv/early/2019/10/29/821439.full.pdf

Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss

Not sure it will work with transcriptome and low-quality genomic data

Speciation in Howea Palms Occurred in Sympatry, Was Preceded by Ancestral Admixture, and Was Associated with Edaphic and Phenological Adaptation

https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msz166/5535536

Related to Rebekah’s work on resolving species complexes. I think it can be improved by having genome data. I don’t really buy their expression analysis

Continued Adaptation of C4 Photosynthesis After an Initial Burst of Changes in the Andropogoneae Grasses

https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syz066/5582656

Genome skimming from herbarium samples for phylogeny and gene family evolution

https://www.sciencedirect.com/science/article/pii/S096098221930939X#sec2

Detecting adaptive evolution from phylo-transcriptomic data: Adaptive Evolution Is Common in Rapid Evolutionary Radiations

https://www.pnas.org/content/115/15/E3471?collection=

Stress experiments across species

Amalgamated cross-species transcriptomes indicate organ-specific 2 preadaptation for functional shifts in gene expression

https://www.biorxiv.org/content/biorxiv/early/2018/09/05/409888.full.pdf 

Do plants have a segregated germline?

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005439