Biology subjects

Smeele, S. Q.

Publications and source records attributed to Smeele, S. Q..

6 recordsLinked to original sources

bioRxiv2023

callsync: an R package for alignment and analysis of multi-microphone animal recordings

O_LITo better understand how vocalisations are used during interactions of multiple individuals, studies are increasingly deploying on-board devices with a microphone on each animal. The resulting recordings are extremely challenging to analyse, since microphone clocks drift non-linearly and record the vocalisations of non-focal individuals as well as noise. C_LIO_LIHere we address this issue with callsync, an R package designed to align recordings, detect and assign vocalisations to the caller, trace the fundamental frequency, filter out noise and perform basic analysis on the resulting clips. C_LIO_LIWe present a case study where the pipeline is used on a dataset of six captive cockatiels (Nymphicus hollandicus) wearing backpack microphones. Recordings initially had drift of [~]2 minutes, but were aligned to within [~]2 seconds with our package. Using callsync, we detected and assigned 2101 calls across three multi-hour recording sessions. Two had loud beep markers in the background designed to help the manual alignment process. One contained no obvious markers, in order to demonstrate that markers were not necessary to obtain optimal alignment. We then used a function that traces the fundamental frequency and applied spectrographic cross correlation to show a possible analytical pipeline where vocal similarity is visually assessed. C_LIO_LIThe callsync package can be used to go from raw recordings to a clean dataset of features. The package is designed to be modular and allows users to replace functions as they wish. We also discuss the challenges that might be faced in each step and how the available literature can provide alternatives for each step. C_LI

ecology↗

bioRxiv2023

Evidence for vocal signatures and voice-prints in a wild parrot

In humans, identity is partly encoded in a voice-print that is carried across multiple vocalisations. Other species also signal vocal identity in calls, such as shown in the contact call of parrots. However, it remains unclear to what extent other call types in parrots are individually distinct, and whether there is an analogous voice-print across calls. Here we test if an individual signature is present in other call types, how stable this signature is, and if parrots exhibit voice-prints across call types. We recorded 5599 vocalisations from 229 individually-marked monk parakeets (Myiopsitta monachus) over a two year period in Barcelona, Spain. We examined five distinct call types, finding evidence for an individual signature in three. We further show that in the contact call, while birds are individually distinct, the calls are more variable than previously assumed, changing over short time scales (seconds to minutes). Finally, we provide evidence for voice-prints across multiple call types, with a discriminant function being able to predict caller identity across call types. This suggests that monk parakeets may be able to use vocal cues to recognise conspecifics, even across vocalisation types and without necessarily needing active vocal signatures of identity.

animal behavior and cognition↗

bioRxiv2022

Multi-level analysis of monk parakeet vocalisations shows emergent dialects between cities in the European invasive range

Geographic differences in vocalisations provide strong evidence for animal culture, with patterns likely arising from generations of social learning and transmission. The current knowledge on the evolution of vocal variation has predominantly focused on fixed repertoire, territorial song in passerine birds. The study of vocal communication in open-ended learners and in contexts where vocalisations serve other functions is therefore necessary for a more comprehensive understanding of vocal dialect evolution. Parrots are open-ended vocal production learners that use vocalisations for social contact and coordination. Geographic variation in parrot vocalisations typically take the form of either distinct regional variations known as dialects or graded variation based on geographic distance known as clinal variation. In this study, we recorded monk parakeets (Myiopsitta monachus) across multiple spatial scales (i.e. parks and cities) in their European invasive range. We then compared calls using a multi-level Bayesian model and sensitivity analysis, with this novel approach allowing us to explicitly compare vocalisations at multiple spatial scales. We found support for founder effects and/or cultural drift at the city level, consistent with passive cultural processes leading to large scale dialect differences. We did not find a strong signal for dialect or clinal differences between parks within cities, suggesting that birds did not actively converge on a group level signal, as expected under the group membership hypothesis. We demonstrate the robustness of our findings and offer an explanation that unifies the results of prior monk parakeet vocalisation studies.

ecology↗

bioRxiv2022

On the use of relative brain size

O_LIThere is a long-standing interest in the effect of relative brain size on other life history variables in a comparative context. Historically, residuals have been used to calculate these effects, but more recently it has been recognised that regression on residuals is not good practice. Instead, absolute brain size and body size are included in a multiple regression, with the idea that this controls for allometry. C_LIO_LII use a simple simulation to illustrate how a case in which brain size is a response variable differs from a case in which relative brain size is a predictor variable. I use the simulated data to test which modelling approach can estimate the underlying causal effects for each case. C_LIO_LIThe results show that a multiple regression model with both body size and another variable as predictor variable and brain size as response variable work well. However, if relative brain size is a predictor variable, a multiple regression fails to correctly estimate the effect of body size. C_LIO_LII propose the use of structural equation models to simultaneously estimate relative brain size and its effect on the third variable and discuss other potential methods. C_LI

evolutionary biology↗

bioRxiv2021

Coevolution of brain size and longevity in parrots

Previous studies have demonstrated a correlation between longevity and brain size in a variety of taxa. Little research has been devoted to understanding this link in parrots; yet parrots are well-known for both their exceptionally long lives and cognitive complexity. We employed a large-scale comparative analysis that investigated the influence of brain size and life history variables on longevity in parrots. Specifically, we addressed two hypotheses for evolutionary drivers of longevity: the Cognitive Buffer Hypothesis, which proposes that increased cognitive abilities enable longer life spans, and the Expensive Brain Hypothesis, which holds that increases in life span are caused by prolonged developmental time of, and increased parental investment in, large brained offspring. We estimated life expectancy from detailed zoo records for 133,818 individuals across 244 parrot species. Using a principled Bayesian approach that addresses data uncertainty and imputation of missing values, we found a consistent correlation between relative brain size and life expectancy in parrots. This correlation was best explained by a direct effect of relative brain size. Notably, we found no effects of developmental time, clutch size, or age at first reproduction. Our results suggest that selection for enhanced cognitive abilities in parrots have in turn promoted longer lifespans.

evolutionary biology↗

bioRxiv2020

Social network architecture and the tempo of cumulative cultural evolution

The ability to build upon previous knowledge--cumulative cultural evolution--is a hallmark of human societies. While cumulative cultural evolution depends on the interaction between social systems, cognition and the environment, there is increasing evidence that cumulative cultural evolution is facilitated by larger and more structured societies. However, such effects may be interlinked with patterns of social wiring, thus the relative importance of social network architecture as an additional factor shaping cumulative cultural evolution remains unclear. By simulating innovation and diffusion of cultural traits in populations with stereotyped social structures, we disentangle the relative contributions of network architecture from those of population size and connectivity. We demonstrate that while more structured networks, such as those found in multilevel societies, can promote the recombination of cultural traits into high-value products, they also hinder spread and make products more likely to go extinct. We find that transmission mechanisms are therefore critical in determining the outcomes of cumulative cultural evolution. Our results highlight the complex interaction between population size, structure and transmission mechanisms, with important implications for future research.

evolutionary biology↗