all them

Level 4. Deep Data (expect this to take at least a few hours, longer if you're inexperienced or if it's a new field; last chance to bail!)

If you want to understand the paper, you have to understand the data, and the only way to understand the data is to spend quality time getting to know it. Figures and tables are the defining elements of research publicationsthey take the raw data generated by researchers' experiments and facilitate analysis of causal relationships through data visualizations (graphs, photos, tables, charts, diagrams, etc). Complete the table in step 5 for every table and figure panel in the paper.

Step 4.1 Go through each figure and table one by one

Figures might be made of multiple panels (usually lettered a, b, c...) which represent different experimental approaches to asking specific questions. For each figure panel, duplicate and complete the table below. Use the Results and/or Methods sections of the paper as a reference to help you understand the figure panels. Sometimes a panel is just a model or structure or diagram that is explanatory but is not testing a causal relationship. When this is the case, summarize the diagram or structure and why it is being shared.

Remember that most science experiments and figures attempt to isolate and measure a causal relationship between one or more independent variables that the researchers vary (often displayed on an X axis) and one or more dependent variable that they measure (often displayed on a Y axis). For an evolutionary genetics paper this might mean comparing a particular gene sequence (dependent variable) in different species or in different genes of the same species (independent variable). Scientists will try to keep as many other variables constant as they can. They will also try to include a positive control (a condition that they know should give a measurable result so they can test their readout and make sure their experiment isn't producing false negatives) and a negative control (a condition that they know should give a negative result so they can make sure their experiment isn't producing false positives).

To interpret a data figure (as opposed to a model or diagram) you should know what the independent (what the scientists change) and dependent (what they measure) variables are, and what the positive (is the method working?) and negative (is the method contaminated or non-selective) controls are.

Panel number and letter (duplicate this table for ALL the panels of ALL the figures!)

Insert screen shot of panel here

What is the independent variable(s) (the one we change)?

What is the dependent variable(s) (the one we measure)

What is the hypothesis being tested (usually a causal relationship, i.e. If X is changed Y will result)?

What, if any, are the positive controls?

What, if any, are the negative controls?

How would you describe the relationship depicted in this panel? For example "If we compare

columns/lines/points __________ and _________, we see the dependent variable

_______________ does ___________.

How does this help the authors answer the specific questions you identified described in 3.4?

Step 4.2 Read the paper (You've already done the hard part! But this will probably still take you an hour or two)

Now that you're an expert in the authors' data, do you agree with their interpretation?

ratio test found that a model with two dN/dS ratios fit the which has been demonstrated to bind to both RNA and A C TBPH 531 aa TBPH RRM1 RRM2 CG7804 RRM1 RRM2 318 aa CG7804 B -Nto A Ato N -Nto B Bto N Ato B -N to N 1 2 16/303 0/123 a -log10 (p-value) millions years ago (Mya) 10/221 7/31 -0.5 0 0.5 0 8 3/7 2/15 100/50 0/35 2/12 0/2 0/9 37/7 29/15 D RRM1 RRM2 0/7 0/2 12/7 5/2 D. erecta D. sechellia D. yakuba D. sechellia D. simulans D. simulans TBPH D. ananassae D. melanogaster D. melanogaster D. pseudoobscura CG7804 TBPH CG7804 FIG. 1. Structural and evolutionary history of CG7804 and TBPH. (A) Exon-intron structure of TBPH (blue) and CG7804 (orange). Filled boxes represent exons (darker color, coding sequence; lighter color, UTRs), whereas lines represent introns. Because CG7804 originated through a retrotransposition event, it lacks most of the introns of TBPH and some of its noncoding sequences do not share homology with TBPH. (B) The duplication event of CG7804 from TBPH is denoted as a dashed line in the phylogeny. The clades of CG7804 and TBPH are in orange and blue, respectively. The number of amino acid substitutions to number of synonymous substitutions inferred by PAML (see text) is denoted at right to branches. The dating of the species phylogeny is from Obbard et al. [2012]. (C) The structures of the amino acid sequences of TBPH and CG7804 areA 0.8- B C 1.00- F 0.8- homozygotes genotype heterozygous KD 0.75- 0.6- 0.6- wildtype nonKD dead pupa eclosion lethal lethality rate percentage 0.4- D.50- dead adult in food 0.4- lethality rate adull unclear 0.25- 0.2- 0.2- n.s. n.s. n.s. I 0.0- I 0.0- 0.00- E to L L to P KD KD nonKD nonkD E to L L to P P to A P to A OP OP developmental stage developmental stage D 1.0- E RNAi gone T1 T2 T3 CG7804 TBPH 0.5- lethality rate 0.0- Downloaded from https://academic.oup.com/ wildtype KD ActSC Tub elav Dll BX salm nub wildtype KD wildtype KD en GAL-4 driver FIG. 2. Stage-specific lethality associated with CG7804 knockdown and knockout. (A) Expression knockdown of CG7804 using Tub-GAL4 driver results in different lethality rates at different developmental stages. (B) Expression knockdown of CG7804 leads to eclosion lethal. (C) The outcome of pupae with CG7804 expression knockdown. (D) CG7804 expression is essential in different tissues from those of its parental gene, TBPH. Lethality rate is significantly different between CG7804 and TBPH knockdown when using elav, Dll, and en GAL4 drivers. Because the lethality rate isGained Developmental Functions of a Young Gene . doi: 10.1093/molbev/msz 137 MBE A B C 25- D 50 75- 2.5 150- " 20- -2.5 50- 15- 100- -log 10(FDR) -log10(FDR) -log 10(FDR) 10- 25- 50- 5- 0- 0- 0- -5 un - -2 2 log2 Fold Change log2 Fold Change log2 Fold Change 1 1,358 / 785 (up) / 1,523 (down) 12,488 / 653 (up) / 139 (down) 12,362 / 462 (up) / 585 (down) E L P 10 EDR (vLee et al. . doi:10.1093/molbev/msz 137 MBE A B C 1.00- 2 insig. TO-71 CG7804 0.75- up regulated proportion down regulated 0.50- [0-7] TBPH 0.25- 0.00- Yes No CG7804 Chip enrichment D E protein-protein F G interaction genetic interaction p = 0.086 0.6- IL 1- 0.3- 40- 0.4- 40- proportion 0- 02- 30- 30- dN/dS 0.2- -1- degree degree 20- 20- 0.1- -2- 0.0- 10- 10- lethal semi-lethal viable -3- 0.0- without CG7804 binding enrichment with CG7804 binding enrichment, no significant differential expression upon CG7804 knockout with CG7804 binding enrichment, significantly higher expression upon CG7804 knockout with CG7804 binding enrichment, significantly lower expression upon CG7804 knockout FIG. 4. Genes with CG7804-binding enrichment are different from other genes in the genome. (A) CG7804 has nuclear localization in the salivary