iiinova — where your digital self keeps evolving

John Alroy @johnalroy.bsky.social · 05/09/2026

The Fossilworks database is now integrated with the Ecological Register and includes growing datasets on Cenozoic and Cretaceous vertebrates including mammals and dinosaurs. All of the 5000+ site inventories include specimen counts used to obtain GW species richness estimates. fossilworks.org

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John Alroy @johnalroy.bsky.social · 05/09/2026

Fitting the geometric Weibull distribution yields low-bias species richness estimates when either museum catalogue data or citizen science observations are analysed: an example involving Australian frogs. New paper in Global Ecology and Biogeography. onlinelibrary.wiley.com/doi/full/10....

onlinelibrary.wiley.com

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John Alroy @johnalroy.bsky.social · 24/12/2025

The Ecological Register now features an interactive mapping tool that lets you find ecological and palaeontological survey data. You can search using Latin names, English names, and time interval names. Click on a link and you can download all the surveys. The home page lists major data sets.

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Reposted by John Alroy

Orlin S Todorov @orlinst.bsky.social · 03/10/2025

Extinct Pleistocene carnivores were diurnal and highly active - fresh off the press 🐯 Only BMR and diurnality are robust predictors of extinction and this also stands for extant species 🦨🐅🦝 With @johnalroy.bsky.social we use an exhaustive sample and account for phylogenetic and trait uncertainty.

https://nsojournals.onlinelibrary.wiley.com/doi/10.1002/ecog.08061

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John Alroy @johnalroy.bsky.social · 13/08/2025

Human impacts on large mammals went well beyond triggering late Quaternary mass extinctions. A new paper by Brook et al. showing that biogeographic patterns were erased by the spread of domesticated species: royalsocietypublishing.org/doi/10.1098/... A related paper is in press. Stay tuned.

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John Alroy @johnalroy.bsky.social · 29/07/2025

Hubbell's neutral model of biodiversity is founded on tree inventory data for Barro Colorado Island – which don't fit the model. A better one is the compound abundance distribution involving the geometric series. A preprint of the newly submitted BCI paper is here: ecoevorxiv.org/repository/v...

ecoevorxiv.org

What's really happening on the Barro Colorado Island 50 ha forest plot?

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John Alroy @johnalroy.bsky.social · 24/07/2025

Shannon's H, Simpson's D, and Pielou's J are useless in ecology. Fitting data with a compound abundance distribution based on the geometric series is a better way to quantify variation – and to estimate species richness. New paper in Ecology Letters. onlinelibrary.wiley.com/doi/10.1111/...

onlinelibrary.wiley.com

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John Alroy @johnalroy.bsky.social · 07/05/2025

Fisher's alpha goes down, not up, as more stems are randomly drawn from across the BCI plot (upper green line). But it goes up if stems are drawn in order going SW-to-NE across the plot (lower). Chao 1 rises steeply (red). CEGS doesn't (upper blue) while capturing the area signal (lower blue).

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John Alroy @johnalroy.bsky.social · 01/05/2025

Methods matter! BCI tree diversity partitioned by size class (5 cm DBH running window). CEGS (blue): flat, then a sudden drop ~40 cm. Chao 1: lower, different, and higher variance. CBR/alpha/theta (orange/purple/pink): ~50% increase on the way up to ~25 cm. But diversity should always decline.

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John Alroy @johnalroy.bsky.social · 30/04/2025

Likelihood differencing is here: the new release of the richness R package for diversity analysis includes an LD version of the CEGS function, which fits species abundance distributions and estimates richness. Check this out if you found my recent preprints interesting. github.com/johnalroy/ri...

github.com

Release Version 3.1 · johnalroy/richness

Version 3.1 of the richness package introduces likelihood differencing with the new cegsLD function. The existing Bayesian and maximum likelihood versions of CEGS (cegsB and cegsML) have been subst...

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John Alroy @johnalroy.bsky.social · 28/04/2025

The BCI manuscript is now done. The log series and ZSM fit the overall 50 ha data poorly. They predict the 1 ha subplot data just as poorly (last post) and underestimate beta diversity (new graph). CEGS is of course best. Manuscript available upon request: comments would be very much appreciated.

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John Alroy @johnalroy.bsky.social · 27/04/2025

CEGS wins again. Predictive test based on the 50 ha BCI tree plot dataset of Hubbell/Foster/Condit (thanks). CEGS fits to species counts in 1 ha plots better predict counts in 9 plots to the east (blue). PLN wins once (red). Log series loses every time. Likelihood ratio cutoff is 10:1.

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John Alroy @johnalroy.bsky.social · 25/04/2025

Rarefaction is also dead – and CEGS gets the job done again. It recovers richness when common species are set aside or when samples are drawn from composite ecological communities. Rarefaction, Shannon's H, and Simpson's D are way off in both cases. www.authorea.com/users/363764...

authorea.com

Coverage-based rarefaction does not quantify species richness

Coverage-based rarefaction (CBR) is a high-profile tool for assessing biodiversity that provides relative species richness estimates. It leverages the Good-Turing index u to interpolate expected richn...

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John Alroy @johnalroy.bsky.social · 22/04/2025

A preprint of a full paper explaining the CEGS distribution model and the way it estimates species richness is now available on EcoEvoRxiv: doi.org/10.32942/X2W... It draws comparisons with other models and estimators including the Poisson log normal, the log series + Fisher's alpha, and Chao 1.

doi.org

A method of predicting ecological community structure

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John Alroy @johnalroy.bsky.social · 20/04/2025

A manuscript about the global consequences of the Late Pleistocene megafaunal mass extinctions, which is now in review. ecoevorxiv.org/repository/v...

ecoevorxiv.org

Late Pleistocene faunal community patterns disrupted by Holocene human impacts

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John Alroy @johnalroy.bsky.social · 19/04/2025

I have just submitted a short paper about the compound exponential-geometric series (CEGS). CEGS predicts count distributions and species richness with high accuracy. A preprint is available upon request.

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John Alroy @johnalroy.bsky.social · 17/04/2025

Evenness is dead. Long live species richness. If you want to use an index, try this R calculation. Where n is a list of species counts: length(n) / mean((n %o% (n - 1))^0.5 / (n %o% n)^0.5) advance.sagepub.com/users/363764...

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