712 BioSci every other week
Date | Presenter and topic | Snack |
1/24 | Jin work updates and grad school interview prep | Ya |
1/30 | Lab group meetings with prospective students | Ya |
2/7 | Aaron practise talk for Cary metabolite joint lab meeting | Precious |
2/13 | Lab group meetings with prospective student | |
3/7 | ||
3/21 | ||
4/4 | ||
4/18 | ||
5/2 | ||
5/16 | Lab field trip? | |
Tree search Model selection vs. model adequacy Consensus Trees and tree support | ||
Bayesian MCMC | ||
Orthology, paralogy | ||
Gene tree/species tree, phylogenetic networks | ||
Molecular dating, hypothesis testing | ||
Comparative methods: character evolution, biogeography, diversification rates | ||
Codon models, molecular evolution |
Journal club questions to guide reading:
We often read papers from seminar speakers before their visit; we also sometimes send the summary to the authors if it is a manuscript on bioRxiv.
Meet in person at 712 BioSci weekly 2:30 pm on Fridays
Presenter | Snack | |
9/20 | Field trip photo show: Precious Iceland conservation workshop; Aaron Utah Eriogonum Society meeting | Aaron |
9/27 | Phylogenetics primer videos Part 1 https://www.youtube.com/watch?v=1r4z0YJq580 | Ya |
Oct 2 | Ya practice talk on Euphorbia | |
Oct 11 | Precious: Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants https://www.nature.com/articles/s41467-024-48036-3 | Precious |
Oct 18 | Homology search and alignment Optimal global pairwise alignment using the Needleman-Wunsch Algorithm (39 min) https://www.youtube.com/watch?v=EWJnDMKBEv0 Optimal local pairwise alignment using Smith-Waterman Algorithm (15 min) https://www.youtube.com/watch?v=YSK0eEoxn9I&t=32s Heuristic local pairwise alignment using BLAST (the most cited yet misunderstood biology paper!) https://pubmed.ncbi.nlm.nih.gov/2231712/ This paper has a lot of math. Don’t spend more than 15-30 min on it. Focus on two questions: Why e-value is not a good representation of relatedness? What other outputs of BLAST other than e-value would be helpful when searching for closely related sequences from a database? Multiple sequence alignment (13 min) https://www.youtube.com/watch?v=CTPiYiTQcuA&t=431s Hopefully these will help you understanding all the algorithm choices in MAFFT https://mafft.cbrc.jp/alignment/software/algorithms/algorithms.html | Ya |
Oct 25 | Aaron practice talk on herbarium spectra for BII meeting | |
Nov 1 | Ya takeaways on ICERM workshop on math problems in phylogenomics https://icerm.brown.edu/video_archive/3856 | Ya |
Nov 15 | Aaron paper on comparative methods | Precious |
Dec 6 | Evolutionary origins, macroevolutionary dynamics, and climatic niche space of the succulent plant syndrome in the Caryophyllales https://doi.org/10.1093/jxb/erae428 | Ya |
Dec 13 | Tree estimation: Distance method (6 min) Neighbor-JoiniDistance Matrix Methods, part 1ng (15 min) Optimizing branch length (22 min) Maximum likelihood (22min) Which algorithms are used most often? What are the scenarios when each is used, and what are the caveats? Briefly go over UPGMA and parsimony. | Precious |
2pm every other Tuesday, 712 BioSci
Presenter | Snack | |
Weeks of Jan 15&22 | Multiple Zoom lab meetings with prospective students | N/A |
1/31 | Lunch to celebrate Alex’s first paper! | N/A |
2/6 | Aaron Polygonaceae research update | Ya |
2/26 | Brett on switch grass GWAS vs. spectra | |
3/18 | Aaron Journal club: Reinventing metabolic pathways: Independent evolution of benzoxazinoids in flowering plants https://www.pnas.org/doi/abs/10.1073/pnas.2307981120 | Aaron |
4/1 | Jeannine papers | Alex |
4/15 | Either Nate Swenson journal club or Aaron/Lauren herbarium spectroscopy updates | |
June | Botany meeting practice talks the week of 10-13. Addison, Lauren (poster), and Alex |
Every other Friday 3pm, 712 BioSci
Presenter | Snack | |
9/15 | Alex practice CFANS seminar | Alex |
9/29 | Aaron field trip slide show + plan for CA field trip | Ya |
10/13 | No lab meeting | |
10/27 | Aaron journal club: Purwadi 2023: Recognition of trace element hyperaccumulation based on empirical datasets derived from XRF scanning of herbarium specimens | |
11/10 | Ya journal club. | |
12/8 | Addison project |
2-3 pm every other Thursday at 818 BioSci
Presenter | Snack | |
6/1 | Diego research | Ya |
6/15 | Lab lunch at Mim’s | |
6/29 | Aaron - Replicated Evolution in Plants | |
7/19 | Botany practice talk round 1: Alex poster, Rebekah talk | Aaron |
7/20 | Botany practice talks round 2: Aaron, Alex talk, Ya talk | Alex |
3-4 pm every other Friday at 818 BioSci
Date | Presenter | Snack |
Feb 3 | updates + SMART goal for the semester. | Ya |
Feb 17 | Alex | Alex |
Mar 3 | Leticia - research | Aaron |
Mar 17 | Rebekah | Rebekah |
Mar 31 | Nicholas, Muna, Annika | |
Apr 14 | Letícia - paper on convergent evolution | |
Apr 28 | Aaron - research | Ya |
May 11 | Rebekah’s practise defense talk (May 15). |
3–4pm every other Friday at 438 BioSci
Nov 11 Innovations and stepwise evolution of CBFs/DREB1s and their regulatory networks in angiosperms https://doi-org.ezp2.lib.umn.edu/10.1111/jipb.13357
Oct 31 (Monday) Rebekah practice talk for the MN Native Plant Society
Oct 14 Aaron - practice prelim & research update
Sep 30 Discuss Leebens-Mack lab papers prior to seminar visit
Sep 16 Ya practice tenure talk
July Botany meeting practise talks
11 am to 12:15 pm every other week at 818 BioSci
Apr 25 Aaron
Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae) https://www.sciencedirect.com/science/article/pii/S0960982220318972
Apr 11 Rebekah on Drosera phylogenomic analyses
Mar 28 Everyone share a paper
Mar 14 Zack on lab safety
Feb 28 Aaron research updates
Feb 14 Aaron Linking the evolution of development of stem vascular system in Nyctaginaceae and its correlation to habit and species diversification
https://evodevojournal.biomedcentral.com/articles/10.1186/s13227-021-00190-1
Jan 31 Ben on rotation project with Candy Hirsch
2pm on Friday every other week
Informal research updates
Dec 3 (moved to 11 am) Marian on cold stress project
Nov 12 Brett on initial analyses on hyperspectral data
Oct 29 Rebekah
Oct 15 Aaron
Oct 11 Ya practice PMB colloquium talk
Oct 1 Outreach activities
Sep 17 Alex and Zack on stress experiment. Slides
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
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)
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
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
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
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!
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
Lab meetings on hold as Ya is teaching and Chen is away
Jan 17 Rebekah practise lightening talk for Bell Advisory Board meeting
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
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
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
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
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
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
https://nph.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/nph.20040
Post-transfer adaptation of HGT-acquired genes and contribution to guanine metabolic diversification in land plants
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
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.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
https://www.science.org/doi/abs/10.1126/science.ade0529
Convergence in carnivorous pitcher plants reveals a mechanism for composite trait evolution