Joseph Matheson
@JosephMatheson2
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Evolutionary biology at UCSD. I-10 fanboy. Easily invested in games of any kind, sci-fi/fantasy, and mashed potatoes.
Joined June 2020
RT @pastramimachine: rather than ruin Thanksgiving dinner by bringing up the election or flouride, why not ruin it by bringing up Neutral T….
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RT @JosephMatheson2: @eigenrobot This thread is ~correct that most discussion of science funding focuses either on 1&3 above (libs) or 8-10….
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RT @JoannaMasel: Our latest preprint finds that a shortage of beneficial mutations does more to drive small populations extinct than mutati….
biorxiv.org
Habitat loss contributes to extinction risk in multiple ways. Genetically, small populations can face an “extinction vortex” — a positive feedback loop between declining fitness and declining...
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RT @opinonhaver: The peaceful existence of Redwall abbey is only possible due to the extreme violence of the Salamandastron military indust….
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RT @alis_harrington: For #fungifriday, we scanned some #herbarium specimens in the U-M Museum of Zoology microCT scanner. Here's my favorit….
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RT @JoannaMasel: Our latest paper on background selection is out at @GenomeBiolEvol. Thread explainers at other 2….
academic.oup.com
Abstract. Background selection describes the reduction in neutral diversity caused by selection against deleterious alleles at other loci. It is typically
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RT @JoannaMasel: Our extensively revised preprint on substitution load is up at Lots of new insights. @JosephMathe….
ecoevo.social
Our extensively revised preprint now goes beyond clarifying Haldane’s arguments about the #CostOfSelection / #SubstitutionalLoad / #SelectiveDeaths, it also significantly extends them, and applies...
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Because the current preprint treats just one locus, it sidesteps the historically critical lag load vs. lead issue, making it unclear how this information theory approach will apply to the realistic case of concurrent sweeps. 11/11.
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The appropriate difference (best existing individual - mean) was rediscovered as the “lead” and put to good use (Desai and Fisher 2007 . Perhaps brighter minds than me could combine geometric fitness, multi-locus lead, and env fluctuation! 10/11.
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This preprint considers just 1 sweep, but load for simultaneous sweeps is where things historically got tricky. Using an optimal pop's fitness as the ref (lag load, following Maynard Smith) isn't right if no optimal individuals exist. (Ewens 1970 9/11.
In the same paper, Haldane also made a flawed load argument where he used the absolute lag load instead of the relative load. Relative load has since been rediscovered as the "lead" q in traveling wave models 3/9
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In the special case of a single stationary environment allowing for perfect adaptation to be optimal, regret is equal to mismatch load, i.e. to Haldane's 1957 equation for the cost of selection. 8/11.
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They define regret as the difference between the average mismatch load of a real population and the mismatch load an optimal population would have experienced. Regret isn't named 'load', but it has more in common with standard load definitions than mismatch load does 7/11.
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The preprint modifies Haldane’s integral to use geometric mean fitness rather than additive (appropriate for comparisons to bacterial growth) and gives it a new name: mismatch load. But its top-level form is still an integral, not a load/difference. 6/11.
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Haldane calls this quantity 'selective deaths' (although it can also be lost reproduction). This illustrative figure (not in preprint shows lost reproduction, but loses the integration concept and doesn't fit Kimura/Haldane formula: cost = -ln(p0). 5/11.
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Confusingly, this version of 'substitution load' isn't actually load, which definition today is generally = a reference fitness minus population mean fitness. Haldane / Kimura 1961 instead integrated q*s over the course of a sweep. 4/11
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This preprint focuses on the substitution load Kimura defines in his 1961 paper, which is identical to the 'cost of selection' Haldane outlines in the main part of his 1957 paper "The Cost of Natural Selection" (. 3/11.
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This theory is notoriously convoluted, however. The term 'substitution load' is especially confusing, because different authors use it to mean different things (Kimura defines it differently between papers!). (see 2/11.
Our latest preprint clarifies @JBS_Haldane's arguments about the cost of selection / substitutional load / selective deaths, and applies the surviving concepts to data @JosephMatheson2 @MExpositoAlonso 1/9.
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Cool preprint by @RS_Mcgee, @livkosterlitz, @evokerr, @kaznatcheev, and @CT_Bergstrom extending the work of Kimura (and by extension Haldane) on substitution load and the cost of natural selection! I love to see a paper modernizing theory from the 1950s. 1/11.
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RT @JoannaMasel: Our latest preprint clarifies @JBS_Haldane's arguments about the cost of selection / substitutional load / selective death….
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