Biology subjects

Somveille, M.

Publications and source records attributed to Somveille, M..

8 recordsLinked to original sources

bioRxiv2024

Consistent and scalable monitoring of birds and habitats along a coffee production intensity gradient

Land use change associated with agricultural intensification is a leading driver of biodiversity loss in the tropics. To evaluate the habitat-biodiversity relationship in production systems of tropical agricultural commodities, which is critical for certifying and examining the success of biodiversity-friendly agricultural practices, birds are commonly used as indicators. However, consistently and reliably monitoring how bird communities are affected by land use change throughout the annual cycle in a way that can be scalable is challenging using traditional survey methods. In this study, we examined whether the automated analysis of audio data collected by passive acoustic monitoring, together with the analysis of remote sensing data, can be used to efficiently monitor avian biodiversity along the gradient of habitat degradation associated with the intensification of coffee production. Coffee is an important crop produced in tropical forested regions, whose production is expanding and intensifying, and coffee production systems form a gradient of ecological complexity ranging from forest-like shaded polyculture to dense sun-exposed monoculture. We used LiDAR technology to survey the habitat, in combination with autonomous recording units and a vocalisation classification algorithm to assess bird community composition in a coffee landscape comprising a shade-grown coffee farm, a sun coffee farm, and a forest remnant, located in southern Mexico. We found that combining LiDAR with the automated analysis of continuously collected bioacoustics data can capture the expected functional signatures of avian communities as a function of habitat quality in the coffee landscape. Thus, we show that this approach can be a robust way to monitor how biodiversity responds to land use intensification in the tropics. A major advantage of this approach is that it has the potential to be deployed cost-effectively at large scales to help design and certify biodiversity-friendly productive landscapes.

ecology↗

bioRxiv2024

National-scale acoustic monitoring of avian biodiversity and phenology

Billions of birds migrate annually, triggered by endogenous behaviors but also by ecoclimatic drivers which are shifting with climate change. These dynamics play out over huge spatiotemporal scales, making monitoring of phenology challenging with traditional biodiversity survey approaches. In this study, over a complete spring migration season (April through June), we collected 37,429 hours of audio from 28 networked sensors in forests across Norway using a nationwide passive acoustic monitoring (PAM) system. We applied an open-source detection algorithm to automatically classify bird vocalizations; through expert validation we found the algorithm classified 57 species (14 full migrants) with at least 80% precision. Using these automated detections, we developed regional arrival curves for three common migratory passerines: Willow Warbler, Common Chiffchaff, and Spotted Flycatcher. We then demonstrate that PAM detections can be used to train audio species distribution models that map how species vocalization probability changes across Norway during spring migration. Lastly, we discuss how PAM can complement existing manual surveys to support the design and implementation of effective policy and conservation measures.

ecology↗

bioRxiv2023

Automatic vocalisation detection delivers reliable, multi-faceted, and global avian biodiversity monitoring

Tracking biodiversity and its dynamics at scale is essential if we are to solve global environmental challenges. Detecting animal vocalisations in passively recorded audio data offers a highly automatable, inexpensive, and taxonomically broad way to monitor biodiversity. However, uptake is slow due to the expertise and labour required to label new data and fine-tune algorithms for each deployment. In this study, we applied an off-the-shelf bird vocalisation detection model, BirdNET, to 152,376 hours of audio comprising of datasets from Norway, Taiwan, Costa Rica, and Brazil. We manually listened to a subset of detections for each species in each dataset and found precisions of over 80% for 89 of the 139 species (100% for 57 species). Whilst some species were reliably detected across multiple datasets, the performance of others was dataset specific. By filtering out unreliable detections, we could extract species and community level insight on diel (Brazil) and seasonal (Taiwan) temporal scales, as well as landscape (Costa Rica) and national (Norway) spatial scales. Our findings demonstrate that, with a relatively fast validation step, a single vocalisation detection model can deliver multi-faceted community and species level insight across highly diverse datasets; unlocking the scale at which acoustic monitoring can deliver immediate applied impact.

ecology↗

bioRxiv2021

Linking animal migration and ecosystem processes: data-driven simulation of propagule dispersal by migratory herbivores

O_LIAnimal migration is a key process underlying active subsidies and species dispersal over long distances, which affects the connectivity and functioning of ecosystems. Despite much research describing patterns of where animals migrate, we still lack a framework for quantifying and predicting how animal migration affects ecosystem processes. C_LIO_LIIn this study, we aim to integrate animal movement behavior and ecosystem functioning by developing a predictive modeling framework that can inform ecosystem management and conservation. Our framework models individual-level migration trajectories between populations seasonal ranges as well as the resulting dispersal and fate of propagules carried by the migratory animals, and it can be calibrated using empirical data at every step of the modeling process. C_LIO_LIAs a case study, we applied our framework to model the spread of guava seeds, Psidium guajava, by a population of migratory Galapagos tortoises, Chelonoidis porteri, across Santa Cruz Island. Galapagos tortoises are large herbivores that transport seeds and nutrients across the island, while Guava is one of the most problematic invasive species in the Galapagos archipelago. C_LIO_LIOur model is able to predict the pattern of spread of guava seeds alongside tortoises downslope migration range, and it identified areas most likely to see germination success and establishment. Our results show that Galapagos tortoises seed dispersal may particularly contribute to guava range expansion on Santa Cruz Island, due to both long gut retention time and tortoises long-distance migration across vegetation zones. In particular, we predict that tortoises are dispersing a significant amount of guava seeds into the Galapagos National Park, which has important consequences for the native flora. C_LIO_LIThe flexibility and modularity of our framework allows for the integration of multiple data sources. It also allows for a wide range of applications to investigate how migratory animals affect ecosystem processes, including propagule dispersal but also other processes such as nutrient transport across ecosystems. Our framework is also a valuable tool for predicting how animal-mediated propagule dispersal can be affected by environmental change. These different applications can have important conservation implications for the management of ecosystems that include migratory animals. C_LI

ecology↗

bioRxiv2021

Post-glacial expansion dynamics, not refugial isolation, shaped the genetic structure of a migratory bird, the Yellow Warbler (Setophaga petechia)

During the glacial periods of the Pleistocene, swathes of the Northern Hemisphere were covered by ice sheets, tundra, and permafrost, leaving large areas uninhabitable for temperate and boreal species. The glacial refugia paradigm proposes that, during glaciations, species living in the Northern Hemisphere were forced southwards, forming isolated populations that persisted in disjunct regions known as refugia. According to this hypothesis, as ice sheets retreated, species recolonised the continent from these glacial refugia, and the mixing of these lineages is responsible for modern patterns of genetic diversity. An alternative hypothesis is that complex genetic patterns could also arise simply from heterogenous post-glacial expansion dynamics, without separate refugia. Both mitochondrial and genomic data from the North American yellow warbler (Setophaga petechia) shows the presence of an eastern and western clade, a pattern often ascribed to the presence of two refugia. However, species distribution modelling (SDM) of the past range of this species fails to identify obvious refugia during the Last Glacial Maximum. Using a climate-informed spatial genetic modelling (CISGeM) framework, which allows us to integrate knowledge of past geographic ranges based on SDM, we reconstructed past population sizes, range expansions, and likely recolonisation dynamics of this species, generating spatially and temporally explicit demographic reconstructions. The model captures the empirical genetic structure despite including only a single, large glacial refugium. The observed contemporary population structure was generated during the expansion dynamics after the glaciation and is due to unbalanced rates of northward advance to the east and west linked to the melting of the icesheets. Thus, modern population structure in this species is consistent with expansion dynamics, and refugial isolation is not required to explain it, highlighting the importance of explicitly testing drivers of geographic structure. Significance statementPatterns of population differentiation in many species have often been attributed to the mixing of isolates from distinct refugia that formed during periods of glaciation, when range fragmentation was likely. By formally bringing together multiple lines of evidence, we demonstrate that the patterns of genetic diversity seen across the range of the yellow warbler (Setophaga petechia) were not the result of multiple isolated refugia. Instead, asymmetric expansion from a single cohesive range generated the observed patterns; the expansions asymmetry was due to the uneven melting of the icesheets over time. Thus, we demonstrate the importance of reconstructing species range dynamics when trying to explain patterns of genetic differentiation.

evolutionary biology↗

bioRxiv2020

The role of habitat configuration in shaping animal population processes: a framework to generate quantitative predictions

By shaping where individuals move, habitat configuration can fundamentally structure animal populations. Yet, we currently lack a framework for generating quantitative predictions about the role of habitat configuration in modulating population outcomes. For example, it is well known that the social structure of animal populations can shape spreading dynamics, but it remains underexplored to what extent such dynamics are determined by the underlying habitat configuration. To address this gap, we propose a framework and model inspired by studies using networks to characterize habitat connectivity. We first define animal habitat networks, explain how they can integrate information about the different configurational features of animals habitats, and highlight the need for a bottom-up generative model that can depict realistic variations in habitat structural connectivity. Second, we describe a model for simulating animal habitat networks (available in the R package AnimalHabitatNetwork), and demonstrate its ability to generate alternative habitat configurations based on empirical data, which forms the basis for exploring the consequences of alternative habitat structures. Finally, we use our framework to demonstrate how transmission properties, such as the spread of a pathogen, can be impacted by both local connectivity and landscape-level characteristics of the habitat. Our study highlights the importance of considering the underlying habitat configuration in studies linking social structure with population-level outcomes.

ecology↗

bioRxiv2019

mtDNA-based reconstructions of change in effective population sizes of Holarctic birds do not agree with their reconstructed range sizes based on paleoclimates

During the Quaternary, large climate oscillations had profound impacts on the distribution, demography and diversity of species globally. Birds offer a special opportunity for studying these impacts because surveys of geographical distributions, publicly-available genetic sequence data, and the existence of species with adaptations to life in structurally different habitats, permit large-scale comparative analyses. We use Bayesian Skyline Plot (BSP) analysis of mitochondrial DNA to reconstruct profiles depicting how effective population size (Ne) may have changed over time, focussing on variation in the effect of the last deglaciation among 102 Holarctic species. Only 3 species showed a decline in Ne since the Last Glacial Maximum (LGM) and 7 showed no sizeable change, whilst 92 profiles revealed an increase in Ne. Using bioclimatic Species Distribution Models (SDMs), we also estimated changes in species potential range extent since the LGM. Whilst most modelled ranges also increased, we found no correlation across species between the magnitude of change in range size and change in Ne. The lack of correlation between SDM and BSP reconstructions could not be reconciled even when range shifts were considered. We suggest the lack of agreement between these measures might be linked to changes in population densities which can be independent of range changes. We caution that interpreting either SDM or BSPs independently is problematic and potentially misleading. Additionally, we found that Ne of wetland species tended to increase later than species from terrestrial habitats, possibly reflecting a delayed increase in the extent of this habitat type after the LGM.

evolutionary biology↗

bioRxiv2018

Movement and conformity interact to establish local behavioural traditions in animal populations

The social transmission of information is critical to the emergence of animal culture. Two processes are predicted to play key roles in how socially-transmitted information spreads in animal populations: the movement of individuals across the landscape and conformist social learning. We develop a model that, for the first time, explicitly integrates these processes to investigate their impacts on the spread of behavioural preferences. Our results reveal a strong interplay between movement and conformity for determining whether local traditions establish across a landscape or whether a single preference dominates the whole population. The model is able to replicate a real-world cultural diffusion experiment in great tits Parus major, but also allows for a range of predictions for the emergence of animal culture under various initial conditions, habitat structure and strength of conformist bias to be made. Integrating social behaviour with ecological variation will be important for understanding the stability and diversity of culture in animals.

animal behavior and cognition↗