DOI: 10.17608/k6.auckland.25549466.v1
title: Vocal learning in a vocal non-learner? Vocal convergence and social proximity shape the calls of the most basal Passeriformes, New Zealand Wrens [Dataset and code]

description: <br>This repository contains the datasets and scripts for the analysis of <b><i>Moran et al. Social proximity and vocal convergence shape the call feature of one of the most basal Passeriformes, New Zealand Wrens. Communications Biology </i></b><b>(2024) 7:575. </b><b><i>https://doi.org/10.1038/s42003-024-06253-y.</i></b><b>Abstract</b>Despite extensive research on avian vocal learning, we still lack a general understanding of how and when this ability evolved in birds. As the closest living relatives of the earliest Passeriformes, the New Zealand wrens (Acanthisitti) hold a key phylogenetic position for furthering our understanding of the evolution of vocal learning because they share a common ancestor with two vocal learners: oscines and parrots. However, the vocal learning abilities of New Zealand wrens remain unexplored. Here, we test for the presence of prerequisite behaviors for vocal learning in one of the two extant species of New Zealand wrens, the rifleman (<i>Acanthisitta chloris</i>). We detect the presence of unique individual vocal signatures and show how these signatures are shaped by social proximity, as demonstrated by group vocal signatures and strong acoustic similarities among distantly related individuals in close social proximity. Further, we reveal that rifleman calls share similar phenotypic variance ratios to those previously reported in the learned vocalizations of the zebra finch, <i>Taeniopygia guttata</i>. Together these findings provide strong evidence that riflemen vocally converge, and though the mechanism still remains to be determined, they may also suggest that this vocal convergence is the result of rudimentary vocal learning abilities.<b>Aim</b>We use an integrative approach that combines machine learning and MCMC GLMM models to test for the presence of vocal production learning in one of the two extant species of New Zealand wrens, the rifleman, <i>Acanthisitta chloris</i>.<b>Results</b>Our results highlight the presence of predispositions for vocal production learning in the rifleman, including group vocal signatures, vocal convergence, and phenotypic variance call ratios similar to vocal learners.<b>Description of the data and file structure</b>Please note: there are two parallel analyses:The first analysis investigates the presence of individual and group vocal signatures using MDS and a random forest and is entitled: <i>vocal_signatures_Communications_Biology</i>The second analysis investigates relationships between acoustic, social and genetic similarity/relatedness and computes the phenotypic variances of rifleman calls. The files related to this analysis are entitled: <i>Input, input_clips_flat, vocal_pedigree.R, and Output.</i><b>Methods</b>For complete methodology, please refer to the <i>Methodology</i> section in <i>Moran et al. Social proximity and vocal convergence shape the call feature of one of the most basal Passeriformes, New Zealand Wrens. Communications Biology </i>(2024) 7:575. <i>https://doi.org/10.1038/s42003-024-06253-y.</i><b>## Audio Input</b>Please note that due to the large size of the raw input audio files, we only provide the clipped annotated audio files instead. For the raw input audio files, please contact the corresponding author.For audio recording use, please receive prior approval from Mana Whenua from the Maungaharuru region, New Zealand - Aotearoa and the Department of Conservation, Aotearoa - New Zealand (Boundary Stream Mainland Island)<b>## Code/Software</b>For code sharing and access, see use conditions below under Code/SoftwareCodes CopyrightLICENSE AGREEMENT- - - -- - - - -All rights reserved.Use and redistributions of the codes is permitted for non-commercial purposes, provided that attribution is given to the copyright holders and authors as follows:<b><i>Moran et al. Social proximity and vocal convergence shape the call feature of one of the most basal Passeriformes, New Zealand Wrens. Communications Biology </i></b><b>(2024) 7:575. </b><b><i>https://doi.org/10.1038/s42003-024-06253-y.</i></b><br>The following conditions must always be met for the code usage:* Redistributions must retain the above copyright notice, this list of conditions and the following disclaimer in the code itself, as well as in documentation and/or other materials provided with the code.* Neither the name of the original author, nor the names of its contributors may be used to endorse or promote products derived from this code without specific prior written permission.THIS CODE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITYAND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIALDAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION). HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS CODE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.<br>