Rare and common vertebrates span a wide spectrum of population trends

The Earth’s biota is changing over time in complex ways. A critical challenge is to test whether specific biomes, taxa or types of species benefit or suffer in a time of accelerating global change. We analysed nearly 10,000 abundance time series from over 2000 vertebrate species part of the Living Planet Database. We integrated abundance data with information on geographic range, habitat preference, taxonomic and phylogenetic relationships, and IUCN Red List Categories and threats. We find that 15% of populations declined, 18% increased, and 67% showed no net changes over time. Against a backdrop of no biogeographic and phylogenetic patterning in population change, we uncover a distinct taxonomic signal. Amphibians were the only taxa that experienced net declines in the analysed data, while birds, mammals and reptiles experienced net increases. Population trends were poorly captured by species’ rarity and global-scale threats. Incorporation of the full spectrum of population change will improve conservation efforts to protect global biodiversity.

A full description of the statistics including central tendency (e.g. means) or other basic estimates (e.g. regression coefficient) AND variation (e.g. standard deviation) or associated estimates of uncertainty (e.g. confidence intervals) For null hypothesis testing, the test statistic (e.g. F, t, r) with confidence intervals, effect sizes, degrees of freedom and P value noted Give P values as exact values whenever suitable.

For Bayesian analysis, information on the choice of priors and Markov chain Monte Carlo settings
For hierarchical and complex designs, identification of the appropriate level for tests and full reporting of outcomes Estimates of effect sizes (e.g. Cohen's d, Pearson's r), indicating how they were calculated

Clearly defined error bars
State explicitly what error bars represent (e.g. SD, SE, CI) Our web collection on statistics for biologists may be useful.

Software and code
Policy information about availability of computer code Data collection

Data analysis
For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors/reviewers upon request. We strongly encourage code deposition in a community repository (e.g. GitHub). See the Nature Research guidelines for submitting code & software for further information.

Gergana Daskalova
All R code used to download and integrate the different open-source databases we used in our analyses is deposited in a GitHub repository. We are happy to grant reviewers and editors access to the repository, and we will make all R code available upon publication. We have archived a library of all of the R packages we used in the specific versions upon which the data collection and database integration are based, and this archive is also included in our GitHub repository.
All statistical analyses were conducted using R version 3.5.1.

April 2018
Data Policy information about availability of data All manuscripts must include a data availability statement. This statement should provide the following information, where applicable: All studies must disclose on these points even when the disclosure is negative.

Study description
Research sample Sampling strategy
Our study aimed to determine if variation in vertebrate population change (trends and fluctuations) is explained by differences in species attributes, such as rarity metrics (geographic range, mean population size and habitat specificity) and conservation status.
A list of all analyses undertaken is available in Supplementary Figure 1 and the structure of our models (including all model terms and their estimates) is presented in Supplementary Tables 2 and 5.
We did not include random effects in the Bayesian models (e.g., a species or region random intercept), because only 28% of the studied species had more than four monitored populations and spatial replication was low (Supplementary Table 1).
We extracted the abundance data for 9284 populations from 2084 vertebrate species from the Living Planet Database (see Table S3 for a list of all species included in our UK-scale analyses, a list of all species in the global analyses is available upon request). We downloaded occurrence data from the Global Biodiversity Information Facility and BirdLife, and information on species habitat preferences and conservation status from the IUCN Red List. We obtained phylogenies for amphibian species from Jetx et al. 2018, for bird species from Jetz et al. 2012, and for reptile species from Tonini et al. 2016.