A unified framework for measuring selection on cellular lineages and traits

Figures

Figure 1

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Figure 2

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Figure 3

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Figure 4 with 1 supplement

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Figure 4—figure supplement 1

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Figure 5 with 2 supplements

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Figure 5—figure supplement 1

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Figure 5—figure supplement 2

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Figure 6

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Figure 7 with 1 supplement

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Figure 7—figure supplement 1

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Appendix 1—figure 1

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Tables

Table 1

	Quantities in lineage statistics	Symbol	Correspondence to $K_X(\xi )$
Fitness	Population growth	$\tau \mathrm{\Lambda }$	$K_X(1)$
	Chronological mean fitness	${⟨h(X)⟩}_{\mathrm{cl}}$	$K_X^{\prime }(0)$
	Retrospective mean fitness	${⟨h(X)⟩}_{\mathrm{rs}}$	$K_X^{\prime }(1)$
	Chronological fitness variance	$\mathrm{Var}{[h(X)]}_{\mathrm{cl}}$	$K_X^{\prime \prime }(0)$
	Retrospective fitness variance	$\mathrm{Var}{[h(X)]}_{\mathrm{rs}}$	$K_X^{\prime \prime }(1)$
Selection strength	Jeffreys divergence bet. $Q_{\mathrm{cl}}(X)$  and $Q_{\mathrm{rs}}(X)$	$S_{\mathrm{JF}}[X]$	$K_X^{\prime }(1)-K_X^{\prime }(0)$
	KL divergence of ${\displaystyle Q_{\mathrm{c}\mathrm{l}}(X)}$ from  ${\displaystyle Q_{\mathrm{r}\mathrm{s}}(X)}$	$S_{\mathrm{KL}}^{(1)}[X]$	$K_X(1)-K_X^{\prime }(0)$
	KL divergence of ${\displaystyle Q_{\mathrm{r}\mathrm{s}}(X)}$ from  ${\displaystyle Q_{\mathrm{c}\mathrm{l}}(X)}$	$S_{\mathrm{KL}}^{(2)}[X]$	$K_X^{\prime }(1)-K_X(1)$
Growth rate gain/loss	Growth rate gain	${\displaystyle S_{\mathrm{K}\mathrm{L}}^{(1)}[D]/\tau \mathrm{\Lambda }}$	$1-K_D^{\prime }(0)/K_D(1)$
	Additional growth rate loss upon perturbation	$-S_{\mathrm{KL}}^{(2)}[D]/\tau \mathrm{\Lambda }$	$1-K_D^{\prime }(1)/K_D(1)$

Table 2

Species	Label	Strain	Medium	Temperature (°C)	Device
E. coli	rpoS-mcherry glucose_30°C	MG1655 F3 rpoS-mcherry /pUA66-PrpsL-gfp	M9 minimal medium +0.2%(w/v) glucose +1/2 MEM amino acids solution (Sigma)	30	Microchamber array	This study
E. coli	rpoS-mcherry glucose_37°C	MG1655 F3 rpoS-mcherry /pUA66-PrpsL-gfp	M9 minimal medium +0.2%(w/v) glucose +1/2 MEM amino acids solution (Sigma)	37	Microchamber array	This study
E. coli	rpoS-mcherry glycerol_37°C	MG1655 F3 rpoS-mcherry /pUA66-PrpsL-gfp	M9 minimal medium +0.1%(v/v) glycerol +1/2 MEM amino acids solution (Sigma)	37	Microchamber array	This study
E. coli	f3nw -sm	F3NW	M9 minimal medium +0.2%(w/v) glucose +1/2 MEM amino acids solution (Sigma)+0.1mM Isopropyl β-D-1 thiogalactopyranoside (IPTG)	37	Agar pad	Nozoe et al., 2017
E. coli	f3nw +sm	F3NW	M9 minimal medium +0.2%(w/v) glucose +1/2 MEM amino acids solution (Sigma)+0.1 mM Isopropylβ-D-1 thiogalactopyranoside (IPTG)+100 μg/ml streptomycin	37	Agar pad	Nozoe et al., 2017
E. coli	f3ptn001 -sm	F3/pTN001	M9 minimal medium +0.2%(w/v) glucose +1/2 MEM amino acids solution (Sigma)+0.1 mM Isopropylβ-D-1 thiogalactopyranoside (IPTG)	37	Agar pad	Nozoe et al., 2017
E. coli	f3ptn001+sm	F3/pTN001	M9 minimal medium +0.2%(w/v) glucose +1/2 MEM amino acids solution (Sigma)+0.1 mM Isopropylβ-D-1 thiogalactopyranoside (IPTG)+200 μg/ml streptomycin	37	Agar pad	Nozoe et al., 2017
M. smegmatis	mc2155 7H9	mc2155	Middlebrook 7H9 medium +0.5% albumin +0.2% glucose +0.085% NaCl+0.5% glycerol +0.05% Tween-80	37	Membrane cover	Wakamoto et al., 2013
S. pombe	EMM28	HN0025	Edinburgh minimal medium +2% (w/v) glucose	28	Mother machine	Nakaoka and Wakamoto, 2017
S. pombe	EMM30	HN0025	Edinburgh minimal medium +2%(w/v) glucose	30	Mother machine	Nakaoka and Wakamoto, 2017
S. pombe	EMM32	HN0025	Edinburgh minimal medium +2%(w/v) glucose	32	Mother machine	Nakaoka and Wakamoto, 2017
S. pombe	EMM34	HN0025	Edinburgh minimal medium +2%(w/v) glucose	34	Mother machine	Nakaoka and Wakamoto, 2017
S. pombe	YE28	HN0025	Yeast extract medium +3%(w/v) glucose	28	Mother machine	Nakaoka and Wakamoto, 2017
S. pombe	YE30	HN0025	Yeast extract medium +3%(w/v) glucose	30	Mother machine	Nakaoka and Wakamoto, 2017
S. pombe	YE34	HN0025	Yeast extract medium +3%(w/v) glucose	34	Mother machine	Nakaoka and Wakamoto, 2017
L1210 mouse leukemia cell	L1210 RPMI-1640	L1210 (ATCC CCL-219)	RPMI-1640 medium (Wako)+10% fetal bovine serum (Biosera) under 5% CO2 atmosphere	37	Mother machine	Seita et al., 2021

Table 3

Species	label	$\tau$(hr)	$t_{\text{start}}$(hr)	$t_{\text{end}}$(hr)	${\displaystyle N_0}$	${\displaystyle N_{\tau }}$
E. coli	rpoS-mcherry glucose_37°C	5	0.95	5.95	163	3989
E. coli	rpoS-mcherry glucose_30°C	8	0.95	8.95	197	6173
E. coli	rpoS-mcherry glycerol_37°C	6.5	0.95	7.45	253	5825
E. coli	f3nw-sm	5	0	5	305	4343
E. coli	f3nw +sm	5	0	5	291	3164
E. coli	f3ptn001-sm	5	0	5	984	9229
E. coli	f3ptn001+sm	5	0	5	977	7429
M. smegmatis	mc2155 7H9	10	1.75	11.75	39	311
S. pombe	EMM28	167	0	167	1148	-
S. pombe	EMM30	131	0	131	963	-
S. pombe	EMM32	123.5	0	123.5	883	-
S. pombe	EMM34	152	0	152	1078	-
S. pombe	YE28	108	0	108	1177	-
S. pombe	YE30	90	0	90	866	-
S. pombe	YE34	78	0	78	863	-
L1210 mouse leukemia cell	L1210 RPMI-1640	60	0	60	474	-

Key resources table

Reagent type (species) or resource	Designation	Source or reference	Identifiers	Additional information
Recombinant DNA reagent	pUA66-PrpsL-gfp (plasmid)	Zaslaver et al., 2006
Strain, strain background (Escherichia coli)	MG1655 F3	Wakamoto lab		MG1655ΔfliCΔfimAΔflu
Strain, strain background (Escherichia coli)	MG1655 F3 rpoS- mcherry /pUA66-P rplS-gfp	Wakamoto lab		MG1655ΔfliCΔfimAΔflu rpoS-mcherry /pUA66-PrplS-gfp

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