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.

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.

Phylogenetic relatedness predicts spatial co-occurrence in Neotropical bats and birds. A new paper by Anikó Tóth with Kate Lyons, Drew Allen, and me. Includes Drew's great new method of inferring interaction processes based on co-occurrence data.

royalsocietypublishing.org/doi/10.1098/...

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...

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/...

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).

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.

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...

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.

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.

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...

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.

A manuscript about the global consequences of the Late Pleistocene megafaunal mass extinctions, which is now in review.

ecoevorxiv.org/repository/v...

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.

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...