DOI: 10.5061/dryad.ghx3ffbq2
title: Trait-habitat associations explain novel bird assemblages mixing native and alien species across New-Zealand landscapes

description: Aim: Species introductions have reshaped island faunas for the last 200
 years, often threatening native biodiversity. Approximately equal numbers
 of native and alien species currently co-occur in the New Zealand
 avifauna, but they show distinct habitat use. Antagonistic interactions,
 habitat affinities and legacies of introduction history may concur to
 explain their segregation along habitat gradients. To investigate these
 processes, we explored how habitat, ecological traits and introduction
 history relate with the current composition of bird assemblages. Location:
 New Zealand Taxon: Birds Methods: We analysed 917 bird point counts spread
 along habitat and elevation gradients in the Canterbury region, South
 Island, and related 10 ecological traits to landscape composition using a
 three-table ordination method known as ‘RLQ analysis’, accounting for
 spatial autocorrelation and phylogeny. We tested whether alien species’
 positions in the RLQ were related to proxies of introduction history.
 Results: Eighteen endemic, 11 native and 19 alien species were distributed
 along a gradient from forest to open-habitat assemblages, in relation to
 foraging mode, nesting site and body size. A second gradient segregated
 species between native and exotic forests according to territoriality,
 sedentarity and diet. Traits accounted for the separation of native and
 alien bird species in forests, but not in open habitats. Phylogenetic
 signals emerged from the separation of native and alien species by forest
 type, and spatial structures suggested a landscape-level, rather than
 regional or local determinism. These correlations were independent of
 introduction history, although open-habitat assemblages tended to host
 alien species introduced later in time.  Main conclusions:
 Habitat type and resource availability explain the spatial partitioning of
 New Zealand bird assemblages between native and alien species more
 consistently than competitive exclusion. We conclude that trait-mediated
 ecological differences among species have likely played a predominant role
 in species’ segregation among landscapes, while maintaining endemic bird
 assemblages in native forests. 
description: All the necessary information with respect to the data is
 provided in the article. It is unwise to use these data without reading
 the article before, and we strongly encourage any user to get in touch
 with us. Raw bird and habitat data are provided for reproducibility, but
 any potential user should keep in mind that they are the property of a
 private institution, Scion Research, which has its own data policy and
 contracts. To comply with these privacy rules, species names have been
 blinded. Hence, the data provided here are sufficient to reproduce
 entirely the analyses performed in the article but not to perform fully
 novel research on this data set.  Corresponding author:
 please contact Jean-Yves Barnagaud: jean-yves.barnagaud@ephe.psl.eu
description: #### Data for : Trait-habitat associations explain novel bird
 assemblages mixing native and alien species across New-Zealand landscapes
 #### These datafiles and R scripts relate to :
 Barnagaud, JY, Brockerhoff,E., Mossion, R., Dufour, P., Pavoine, S.,
 Deconchat, M. & Barbaro, L. 2021. Trait-habitat associations
 explain novel bird assemblages mixing native and alien species across
 New-Zealand landscapes. Diversity & Distributions. 
 All the necessary information with respect to the data is
 provided in the article, but species names are blinded. It is unwise to
 use these data without reading the article before, and we strongly
 encourage any user to get in touch with us ahead. The original bird count
 and habitat data are supplied for reproducibility but their public use and
 diffusion is subject to the contractual rules and authorization of Scion
 Research, Christchurch, NZ. Please contact Eckehard Brockerhoff
 (eckehard.brockerhoff@gmail.com) or Jean-Yves Barnagaud
 (jean-yves.barnagaud@ephe.psl.eu) if you are willing to re-use these data.
 Only the raw data that are necessary to replicate the analyses of the
 above-mentioned article are provided here. They are not sufficient to
 engage into a fully new study.  #### Authors
 #### Jean-Yves Barnagaud (1)* –
 jean-yves.barnagaud@ephe.psl.eu (corresponding author)<br> ORCID:
 https://orcid.org/0000-0002-8438-7809<br> Eckehard G. Brockerhoff
 (2,3)*<br> Raphael Mossion (1)<br> Paul Dufour (4)<br>
 Sandrine Pavoine (5)<br> Marc Deconchat (6)<br> Luc Barbaro
 (5,6)<br> * equal contributions<br>  <br> ####
 Corresponding author #### Please contact Jean-Yves
 Barnagaud : jean-yves.barnagaud@ephe.psl.eu<br>  <br> ####
 Usage notes #### Species, variables and traits acronyms
 are defined in the article. The data files have been blinded to comply
 with Scion Research's data privacy rules. ####
 List of files #### ## Folder “data” contains all the
 necessary data to replicate the analyses (except species' names which
 are blinded).  traits_bird_NZ_bin_blinded.txt and
 Q_blinded.txt : these two matrices contain bird trait data with different
 formatting. The two files originate from Q.txt but are provided twice to
 facilitate the run of R codes. Authors : Jean-Yves Barnagaud &
 Raphaël Mossion. species-status_blinded.txt : species
 status and biome of origin (compilation from literature sources). Author :
 Jean-Yves Barnagaud R.txt : Habitat on point counts.
 The first column contains point count indices for correspondence with
 L.txt and geographic_coordinates.txt. Author : Eckehard Brockerhoff. Note
 : these data are owned by a private company, Scion Research, which has its
 own data policy. They should not be reused for new studies without their
 permission, to be applied for through E. Brockerhoff.
 NZBirds_Prum_blinded.tre : Phylogenetic tree for the species
 considered in the study. Author : Paul Dufour
 (paul.dufour80@gmail.com) L_blinded.txt : Bird counts
 per point. Author : Eckehard Brockerhoff. Note : these data are owned by a
 private company, Scion Research, which has its own data policy.
  Species' names are blinded. They should not be reused for new
 studies without their permission, to be applied for through E.
 Brockerhoff. Introduction_effort_blinded.txt : data on
 the number of introduction events and introduction effort. Author: Raphaël
 Mossion.  hab.txt: forest category at each point count.
 Author : Raphaël Mossion. These categories are derived from
 R.txt geographic_coordinates.txt: geographic
 coordinates of point counts (EPSG27200-NZGD49). Author : Eckehard
 Brockerhoff. Note : these data are owned by a private company, Scion
 Research, which has its own data policy. They should not be reused for new
 studies without their permission, to be applied for through E.
 Brockerhoff ## Folder “scripts” contains all the
 necessary data to replicate the analyses. <br>
 Barnagaud_et_al_div_dis_2021_blinded.R : R script to replicate all the
 analyses described in the article. Authors : Raphaël Mossion and Jean-Yves
 Barnagaud<br> functions_Barnagaud_DD_2021.R : additional functions
 adapted from Pavoine et al, 2011. Authors : Raphaël Mossion and Sandrine
 Pavoine.