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John Benning

@jbenning.bsky.social

We thank our generous colleagues across various disciplines whose feedback helped improve this work.

November 7, 2025 at 7:06 PM

John Benning

@jbenning.bsky.social

(iii) how confounding is obscured or even leveraged in a broader class of contemporary genetic studies. In particular, we discuss where claims about genetic causality may reach beyond the evidence.

Confounding among families induces biases in genome wide association studies (GWAS). ‘Population structure confounding’ in genomic data relates to correlations between the structure of genetic relatedness in a GWAS sample (exemplified by the orange-to-purple gradient) and the phenotype studied. Here we show genetic sequences from individuals 1−4 at top left, with their attendant phenotypes (height) at top right. For a given genetic variant, individuals with purple alleles will tend to be taller than those with orange alleles, regardless of the variant’s causal effect on height. This confounding affects any variants that reflect this axis of genetic population structure—typically many millions of variants. While researchers often use methods that adjust for population structure in an attempt to avoid spurious associations, the extent of residual confounding in GWAS remains unclear.

November 7, 2025 at 7:06 PM

John Benning

@jbenning.bsky.social

(ii) a study by Song & Zhang (2024) purporting to solve a paradox: the evolutionary maintenance of genetic variants that increase same-sex sexual behavior, despite being “reproductively disadvantageous.”

(a) Song & Zhang [32] show that the estimated genetic correlation between BSB (a measure of bisexual behaviour) in males and number of children is significantly different from zero (left diagram). They hypothesized the causal structure shown in the right diagram: genetic variants affecting BSB affect the number of children only through their simultaneous effect on risk-taking behaviour. When adjusting for genetic effects on risk-taking behaviour, the partial (residualized) genetic correlation between BSB and number of children is no longer significantly non-zero. They take this observation as evidence for their hypothesis. (b) When we repeat this analysis but replace risk taking with a variety of other measures (‘measure X,’ blue in causal diagram), 16 out of 18 measures we examined yield a partial genetic correlation between BSB and number of children that does not significantly differ from zero (bars show 95% confidence intervals). Therefore, the data are equally consistent with the hypothesis that genetic variants driving BSB are maintained through evolution as a byproduct of selection on any of these 16 measures. We note that most of these measures—like risk-taking behaviour—have a significant partial genetic correlation with number of children. Four of the measures, denoted with an asterisk, are not. (c) Male participants in the study sample who reported having first had sex before the age of 13 (including victims of childhood sexual assault, many of which would have had same-sex perpetrators) are likelier to be classified as BSB by the criteria used in Song & Zhang [32]. N, total number of males in each group.

November 7, 2025 at 7:06 PM

John Benning

@jbenning.bsky.social

(i) a study by Clark (2023) suggesting that patterns of similarity in social status between relatives indicate that social status is largely determined by one’s DNA

Confounding between genetic and non-genetic factors influencing traits. (a) Confounding within families. Non-genetic transmission can parallel genetic transmission and their respective effects are confounded in observational data. Illustrated is a model where a trait value is the sum of an inherited component from parents and random noise. Under this model, the expected resemblance between relatives depends on transmissibility (t2, the portion of trait variation attributable to the transmitted component) and a rate of decay across genealogical distance (the ‘persistence rate,’ b, which increases with increasing degree of assortative mating). Ignoring the confounding of genetic and non-genetic transmission in the data, Clark [3] misassigns all transmission as genetic heritability and all assortative mating to be on a latent ‘social genotype’.

Reanalyses of data from Clark [3] challenge the paper’s claims. (a) Example of confounding between genetic and non-genetic transmission. The relationship between paternal wealth and a measure of social status suggest at least one source of confounding between genetic and non-genetic transmission. Across relative pairs, correlation in occupational status is highly correlated (Pearson’s r = 0.91) with those relatives’ correlation in paternal wealth. Inset shows that individual occupational status is strongly correlated (Pearson’s r = 0.72) with father’s wealth. (b) Pseudoreplication distorted estimates of familial correlations. Familial correlations (95% confidence interval (CI)) in occupational status (1780−1859) using the approach employed by [3] (in gold) involved pervasive, non-uniform pseudoreplication (electronic supplementary material, note S6). For example, the (1780−1859) occupational status correlation for fourth cousins is calculated from 17 382 pairs, derived from only 1878 unique individuals. In teal we show conservative estimates using only a single relative pair per surname (means and 95% CI over 1000 bootstrap samples are plotted for each familial correlation), which are therefore not susceptible to pseudoreplication. Distant cousins show dramatically higher correlations after adjusting for pseudoreplication. (c) Signals of change in social mobility. Parent-offspring correlations in multiple status measures generally decrease over time in Clark’s [3] data, in contrast to claims of stagnant social mobility made in the original paper. To mitigate pseudoreplication, we calculated correlations using one pair from each surname (as in (b)). Shown are average correlations (95% CI) across 500 bootstrap iterations of correlation estimation. The electronic supplementary material, figure S13 shows two complementary analyses estimating correlations either without accounting for pseudoreplication, or using percentile ranks—both result in similar trends.

November 7, 2025 at 7:06 PM

John Benning

@jbenning.bsky.social

made a few updates to the EcoEvo Jobs app -- a lil more data, marginal histograms and, for the masochists, the ability to plot your own stats for comparison 🙃

Check it out here:
john-benning.shinyapps.io/shiny/

January 2, 2024 at 9:57 PM

John Benning

@jbenning.bsky.social

even better, can give you real data! 😁 here, the two pops/sites are Center and Edge, and we have trait (fitness) data for parental lines and various crosses (which allows us to get varying combinations of nuclear and cytoplasmic genomes)

December 29, 2023 at 5:34 PM

John Benning

@jbenning.bsky.social

Do you think about range expansions, dispersal evolution, invasions?? Check out our new preprint:

"Environmental gradients mediate dispersal evolution during biological invasions" doi.org/10.1101/2023...

Environmental gradients oppose the evolution of increased dispersal during range expansion. Results of 1000 simulations after 200 generations of expansion. (a) Illustrates the mean dispersal phenotype within core and edge regions plotted against spatial gradient slope. Core and edge regions comprise the five most proximate and distal patches to the founding patch, respectively. The dashed line signifies the mean dispersal of the founding populations at the start of expansion. (b) Depicts the difference in dispersal between the core and edge across gradient slopes, expressed as the absolute increase in mean dispersal ability of the edge relative to the core. To aid in interpretability, (c) shows dispersal difference plotted against dispersal cost instead of gradient slope. Dispersal cost is a function of gradient slope and the strength of selection, and is the expected decrease in P(survival) for an individual perfectly adapted to patch x dispersing to patch x+1.

December 18, 2023 at 5:22 PM

John Benning

@jbenning.bsky.social

If you have two or more bug species in one shot, let's see em
(you have to look carefully to find #2 here 😉)

November 28, 2023 at 5:17 PM

John Benning

@jbenning.bsky.social

We examine other critical issues with C23, such as the misconstrual of model parameters and the effect of statistical artifacts on all inferences drawn in the paper.

Familial correlations in occupational status (1780-1859) using the approach employed by C23, which involved pervasive pseudo-replication, versus a conservative estimate that did not, using only a single relative pair per surname (mean estimate over 1000 bootstrap samples is plotted for each familial correlation). Distant cousins show dramatically higher correlations when adjusting for pseudo-replication.

Changes in parent-offspring correlations over time contradict C23's claims of stagnant patterns in familial correlations. (a) Occupational status 1780-1919; (b) higher education 1780-1919; (c) literacy 1740-1879. To mitigate pseudo-replication, we calculated correlations using one pair from each surname. Shown are average correlations across 500 bootstrap iterations of correlation estimation. Fig. S13 shows two complementary analyses where correlations are estimated either without accounting for pseudo-replication, or using percentile ranks—both result in similar trends.

November 3, 2023 at 6:31 PM

John Benning

@jbenning.bsky.social

Examining one example of a non-genetic factor known to influence socioeconomic status, paternal wealth, we see evidence of substantial confounding in the C23 data.

An individual’s occupational status is strongly correlated with the wealth of their father. (a) Offspring occupational status is well predicted by paternal wealth. This suggests at least one source of confounding between genetic and non-genetic transmission. (b) Relative correlations in occupational status are highly correlated with those relatives’ correlation in paternal wealth.

November 3, 2023 at 6:29 PM

John Benning

@jbenning.bsky.social

However, along with genes, ancestors transmit wealth, material conditions, knowledge, culture, and many other factors influencing social outcomes. Crucially, we show that C23 does not grapple with the inherent confounding between genetic and non-genetic transmission.

Illustration of how transmissibility (t^2) and rate of decay of correlations across generations (the “persistence rate,” b) influence trait resemblance between relatives in the model used by C23. b will increase as assortative mating increases. Ignoring the confounding of genetic and non-genetic transmission in the data, C23 misassigns all transmission as genetic heritability and all persistence due to assortative mating to be due to spousal correlation with respect to a latent genetic factor.

November 3, 2023 at 6:29 PM

John Benning

@jbenning.bsky.social

Based on correlations between English relatives in measures of social status, C23 argued that social mobility has been stagnant for centuries despite social changes, and that this is due to the near-deterministic genetics of status and assortative mating on a “social genotype.”

November 3, 2023 at 6:28 PM

John Benning

@jbenning.bsky.social

Wide-footed Treehopper looking cute as hell. A beautifully diverse group, treehoppers feed on plant sap, with many producing honeydew that's eaten by their ant mutualist pals. #insects #BackyardNaturalHistory 🌿

September 19, 2023 at 2:19 AM

John Benning

@jbenning.bsky.social

Theo's first camping trip (in the backyard 😂)

September 14, 2023 at 2:03 PM

John Benning

@jbenning.bsky.social

A new wasp species for the yard today -- the Beewolf 🐺 (Philanthus gibbosus most likely), foraging on Ontario Aster. Females hunt bees, which they paralyze with venom before dragging back to their tunnel for their young to (eventually) feast on.
#backyardNaturalHistory #insects #phonemacro

September 14, 2023 at 2:35 AM

John Benning

@jbenning.bsky.social

A classic autumnal scene: Bombus impatiens snoozing on Smooth Blue Aster. Unlike almost all other insects, Bombus are heterothermic -- tho usually functioning as ectotherms, they can elevate their body temperature endogenously when needed. #backyardNaturalHistory

September 11, 2023 at 2:29 PM

John Benning

@jbenning.bsky.social

My little mariposa at the Monarch festival yesterday in Minneapolis

September 10, 2023 at 2:16 PM

John Benning

@jbenning.bsky.social

Oh to be the first bee on the flower in the morning, getting that fresh nectar and pollen

September 9, 2023 at 3:20 PM

John Benning

@jbenning.bsky.social

Parker's Thread-waisted Wasp (Prionyx parkeri) waiting for the sun's warmth this morning in the backyard prairie. Females paralyze grasshoppers and bury them in burrows to feed their developing young 🤘
🌍🧪

September 8, 2023 at 2:11 PM

John Benning

@jbenning.bsky.social

Throwback to when I worked with birds 😂 #ecology 🌍🧪

September 6, 2023 at 4:42 PM

John Benning

@jbenning.bsky.social

You can find so many different insects sipping from the extra-floral nectaries on Partridge Pea (Chamaecrista fasciculata). Watching my Cf patch while drinking my coffee in the morning is prime natural history entertainment