Article commentary

Editors can now comment on articles published in PeerJ and elsewhere.

Species turnover reveals hidden effects of decreasing nitrogen deposition in mountain hay meadows (2019) PeerJ

Douglas Burns –– Roth et al. present results of an analysis of change in vascular plant community structure at 129 sites in Switzerland over a 15-year period (2003-17) during which atmosp... Read more

Using observation-level random effects to model overdispersion in count data in ecology and evolution
311 citations · 17,302 views · 4,178 downloads
Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences
271 citations · 18,957 views · 3,738 downloads
Swarm: robust and fast clustering method for amplicon-based studies
252 citations · 14,634 views · 2,135 downloads
De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
110 citations · 10,527 views · 1,974 downloads
Humans differ in their personal microbial cloud
105 citations · 52,147 views · 5,574 downloads
Automatic large-scale classification of bird sounds is strongly improved by unsupervised feature learning
104 citations · 18,308 views · 2,697 downloads
Continent-wide survey reveals massive decline in African savannah elephants
88 citations · 41,820 views · 4,973 downloads
A brief introduction to mixed effects modelling and multi-model inference in ecology
80 citations · 35,105 views · 8,364 downloads
Gooseneck barnacles (Lepas spp.) ingest microplastic debris in the North Pacific Subtropical Gyre
79 citations · 11,830 views · 1,986 downloads
A comparison of observation-level random effect and Beta-Binomial models for modelling overdispersion in Binomial data in ecology & evolution
70 citations · 6,476 views · 1,570 downloads

Discussing these articles

I'm late to the party. Just found another #amplicon #clustering approach - interesting, but already from 2014: "Swarm: robust and fast clustering method for amplicon-based studies" by Mahé et al.

@pjacock @torstenseemann Not blast exactly but we found it mattered for usearch when reference contained duplicate/similar sequence s

It’s finally out! A Brief Introduction to Mixed Effects Modelling and Multi-Model Inference, published today in @thePeerJ #Ecology #EvolutionaryStudies #Statistics

@larcilah @HideInamine @TigrerosNatasha @slaubrie @kdhecology @bolkerb Sounds good! Looks like implementation is easy (just add another random effect and use poisson family), and here's a recent paper talking about the usefulness and limitations of this approach:

Automatic large-scale classification of bird sounds is strongly improved by unsupervised feature learning - probably the way to go for #bioacoustic #monitoring

Observation Level Random Effects in Overdipsersed Binomial Mixed Models via @thePeerJ

@ejame16 Not completely environmental, but this one had a high wow factor: tpersonal microbial cloud. PeerJ3:e1258

African Elephant (Loxodonta africana) Populations Crash! Article: Journal:

Los elefantes africanos al borde de la extinción - In Spanish

Daily Maverick: "Counting Africa’s beleaguered elephants: Massive two-year census finds alarming declines"

GeekWire: "Paul Allen’s Great Elephant Census confirms catastrophic decline in Africa"

The Washington Post: "The largest-ever survey of elephants in Africa reveals startling declines"

Huffington Post: "A New Elephant Census Shows The Devastating Impact Of Poaching"


NPR Radio Slot: "Often On The Move, Restless Elephants Are Tough To Count — And Keep Safe"

NPR: "African Elephant Population Declines By 30 Percent"

Mashable: "Historic census reveals the true plight of Africa's elephants"

The Guardian: "Poaching drives huge 30% decline in Africa's savanna elephants"