Latest Articles

• 

  Section: Forest & Wood Sciences ; Topics: Ecology, Statistics

  Informative priors contribute to quantifying the occurrence rate of a rare tree-related microhabitat in a managed forest

  Cottais, Pierre;   Courbaud, Benoît;   Larrieu, Laurent;   Gouix, Nicolas; Laroche, Fabien  

  10.24072/pcjournal.697 - Peer Community Journal, Volume 6 (2026), article no. e33

  Get full text PDF

  Tree-related microhabitats (TreMs) are key features for forest biodiversity, and knowing their accumulation rate is essential to design integrative management strategies. Many types of TreMs are associated to large old trees and show slow ontogenical processes. The rarity of such TreMs (particularly in intensively managed forests) hinder the estimation of their occurrence rate along tree growth. Here, we used a continental meta-analysis on TreMs occurrence rate along tree growth to build informative priors for a model of trunk-base rot-hole occurrence on oaks within the Grésigne forest, France --- a context where stand management and tree DBH were confounded. We explored whether the use of informative priors could improve the identifiability, the precision of estimates and the predictive abilities of the model. Without prior information, the low variance of tree DBH within management modalities rendered the model poorly identifiable and prevented the detection of an effect of tree DBH per se across the range of explored tree DBH. By contrast, using informative priors contributed to improve the precision of estimates and lead to detecting a positive effect of tree DBH per se.  Informative priors did not degrade the model fit and clearly improved predictive abilities on new stands. In particular, while the model without prior information did not predict the occurrence of trunk-base rot-holes significantly better than a purely random guess, the model with informative priors did. Irrespective of the prior used, models suggested that the high recruitment of trunk-base rot-holes in Grésigne may be a temporary management effect in stands undergoing conversion from coppice-with-standards to high forest through sprout thinning, which will lead to conservation issues for cavicolous saproxylic species when all conversions are complete. Because using informative priors was simple and beneficial in our study, it should be further explored in other local applied contexts to orientate forest management.

• 

  Section: Ecology ; Topics: Ecology

  Are all waterholes equal from a lion’s view? Exploring the role of prey abundance and catchability in waterhole visitation patterns in a savannah ecosystem

  Dejeante, Romain;   Loveridge, Andrew J.; Macdonald, David W.; Madhlamoto, Daphine; Chamaillé-Jammes, Simon;   Valeix, Marion  

  10.24072/pcjournal.705 - Peer Community Journal, Volume 6 (2026), article no. e32

  Get full text PDF

  Prey abundance and catchability shape the spatial ecology of predators. Predators can select habitats where prey are more abundant to maximize encounter rate with prey or habitats where prey are more catchable to maximize prey capture. These hypotheses are commonly referred to as prey-abundance and prey-catchability hypotheses. Although these hypotheses are often tested at the landscape scale, little is known about how between-patch variations in prey abundance and catchability determine the space use of predators. In many savannah ecosystems, large herbivores aggregate around waterholes, which become hotspots of prey and their selection by predators is classically interpreted as supporting the prey-abundance hypothesis. Here, we investigated whether between-waterhole variations in prey abundance and catchability influence the frequency and duration of lion visits to waterholes, testing the prey-abundance and prey-catchability hypotheses at the resource-patch scale. We combined datasets on (1) lion movements recorded from GPS collars deployed on 20 adult males and 16 adult females between 2002 and 2015, (2) prey abundance evaluated from long-term, regular monitoring of waterholes and (3) prey catchability evaluated from remote-sensing satellite imagery of vegetation cover around waterholes in Hwange National Park (Zimbabwe). Lions did not use all waterholes in their territory equally: there was a high variability in the frequency and duration of visits. Surprisingly, between-waterhole variations in prey abundance and catchability only slightly explained these variations in frequency – and even less in duration – of lion visits to waterholes. Yet, the frequency of lion visits to waterholes decreased with the number of waterholes within their territory, and male lions more frequently visited the waterholes surrounded by more open habitats. We discuss the limits of our work, but also the ecological mechanisms that may explain these findings. First, lions and their prey are involved in a ‘shell-game’ that leads them to adopt unpredictable movement strategies. Second, lions have only access to a limited number of waterholes amongst which to distribute their hunting effort. Lastly, lions visit waterholes not only to hunt but also to interact with social mates and competitors. This work challenges the implicit assumption that all waterholes are the same from a lion’s view and calls for further studies investigating the drivers of the variability in lion visits at the resource-patch scale.

• 

  Section: Microbiology ; Topics: Microbiology

  Cenote-Taker 3 for fast and accurate virus discovery and annotation of the virome

  Tisza, Michael J.;   Varsani, Arvind;   Petrosino, Joseph F.;   Cregeen, Sara J. Javornik  

  10.24072/pcjournal.706 - Peer Community Journal, Volume 6 (2026), article no. e31

  Get full text PDF

  Viruses are abundant across all Earth's environments and infect all classes of cellular life. Despite this, viruses are something of a black box for genomics scientists. Their genetic diversity is greater than all other lifeforms combined, their genomes are often overlooked in sequencing datasets, they encode polyproteins, and no function can be inferred for a large majority of their encoded proteins. For these reasons, scientists need robust, performant, well-documented, extensible tools that can be deployed to conduct sensitive and specific analyses of sequencing data to discover virus genomes - even those with high divergence from known references - and annotate their genes. Here, we present Cenote-Taker 3. This command line interface tool processes genome assemblies and/or metagenomic assemblies with modules for virus discovery, prophage extraction, and annotation of genes and other genetic features. Benchmarks show that Cenote-Taker 3 outperforms most tools for virus gene annotation in both speed (wall time) and accuracy. For virus discovery benchmarks, Cenote-Taker 3 performs well compared to geNomad, and these tools produce complementary results. Cenote-Taker 3 is freely available on Bioconda, and its open-source code is maintained on GitHub (https://github.com/mtisza1/Cenote-Taker3).

• 

  Section: Registered Reports ; Topics: Psychological and cognitive sciences

  Higher Pitch, Slower Tempo, and Greater Stability in Singing than in Conversation among Mandarin speakers in Auckland: A Registered Report Replicating Ozaki et al. (2024)

  Jia, Zixuan;   Purdy, Suzanne C.;   Savage, Patrick E.  

  10.24072/pcjournal.698 - Peer Community Journal, Volume 6 (2026), article no. e30

  Get full text PDF

  Cross-cultural research led by Ozaki et al. (2024) has revealed that songs exhibit higher pitch, lower tempo, and more stable pitches than speech. However, this research relied on solo recordings, while most singing and speaking occurs in group contexts. The present study examined the acoustic features of speech and songs among Mandarin speakers in group settings. We addressed two questions: 1 [confirmatory]) Do singing and conversation in group contexts show similar acoustic patterns to those reported by Ozaki et al. (2024)? 2 [exploratory]) Does musicianship relate to the acoustic differences between speech and song? Three groups of native Mandarin speakers (n = 20) in Auckland participated in the singing and conversation tasks (both of which involved taking turns alternating singing/speaking). We analyzed three acoustic features (pitch height, temporal rate, pitch stability) to test the confirmatory question and examined correlations between musicianship and effect sizes for the exploratory question. Our confirmatory analyses replicated and extended the findings of Ozaki et al. (2024), showing that singing exhibited significantly higher pitch (D = 1.21), slower tempo (D = 2.07), and more stable pitch (D = 0.57) than conversation among Mandarin speakers. Exploratory results suggested a trend whereby individuals with higher musicianship tended to produce greater acoustic differentiation between speech and song; additional data are needed to confirm this effect. In future work, our team will integrate data from up to 26 languages/sites included in the Stage 1 Programmatic Registered Report protocol and conduct meta-analyses to provide more comprehensive estimates of cross-cultural relationships between speech and song.