Summer 2020

Via zoom every two weeks, 1pm on Fridays May 29-Jul 10

Botany talk prep

Jul 10

Jun 26

Jun 12 Rebekah and Diego

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

Botany title submission deadline May 31

Previous semesters

Spring 2020

Via zoom 1pm weekly on Fridays

May 8 Postdoc job candidate

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

Everyone share their own tips

Everyone share a paper they read

Small useful linux tools

awk

screen

Papers for the future (feel free to add)

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

Harmon book from Chapter 9?

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 

Stenz 2015 SysBio

Exploring Tree-Like and Non-Tree-Like Patterns Using Genome Sequences: An Example Using the Inbreeding Plant Species Arabidopsis thaliana (L.) Heynh

https://academic.oup.com/sysbio/article-lookup/doi/10.1093/sysbio/syv039