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Section: Animal Science ; Topics: Agricultural sciences, Applied biological sciences

Shade use, welfare and performance of ewes grazing in temperate silvopastures differing in tree density

Ginane, Cécile; Bernard, Mickaël; Deiss, Véronique; Andueza, Donato; Béral, Camille

10.24072/pcjournal.538 - Peer Community Journal, Volume 5 (2025), article no. e39.
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The study aimed to objectify the importance of trees for sheep welfare by characterising how productive ewes, grazing in temperate mid-mountain pastures, use shade depending on climatic conditions and tree density. The impact of trees on sheep performance was also investigated. We hypothesised that ewes would actively seek out tree shade, due to its mitigating effect on heat stress, and that this active search would intensify as climatic conditions became more stressful. We also hypothesised that their motivation to seek shade would become more pronounced as the availability of shade, i.e. the density of trees, decreased. The experimental design included three permanent pastures with either one tree (Tlow; 0.8% of the pasture area), 60 trees/ha (Tmed; 40%) or 150 trees/ha (Thigh; 81%). Each pasture was continuously grazed by ten Romane ewes and their twin lambs until weaning, for three consecutive years in spring and summer. Ewes’ posture, activity and positioning relative to shade were recorded by scan sampling over a total of 12 sunny days (6-7.5 h/d). On these days, ewes’ respiratory rates were recorded. A nearby weather station allowed for the climatic characterisation of the observation days (combination of temperature, radiation and humidity in a synthetic variable: TRH). Logically, ewes spent more time in shade as tree density increased, from 44% of scans in Tlow to 83% in Thigh across all days. Although the observation days appeared to be low stressful according to classical heat stress indices, the ewes increased the proportion of time spent in shade as climatic conditions worsened (increasing risk of heat stress), by 122% in Tlow, 44% in Tmed and 11% in Thigh, according to shade use estimates between TRH values of 0 and 2.5. Ewes also showed greater selectivity for shade at low tree densities, as indicated by the Jacobs’ Selectivity Index values of 0.93 for Tlow (44% of time in shade relative to 0.8% canopy cover), 0.59 for Tmed (73% relative to 40%) and 0.12 for Thigh (83% relative to 81%). Hence, the ewes actively sought out tree shade, even on days with lower TRH. This highlights the importance of shade provision at pasture for sheep welfare, and suggests that active shade seeking may be an indicator of increasing thermal load. Shade selection was maximal for resting and ruminating (up to 100% of these activities being spent under shade, including by Tlow ewes) but also occurred for feeding at medium tree densities (Tmed). Respiratory rates were slightly lower in wooded plots (55.0 movements/min in Thigh and 63.3 in Tmed, compared to 76.4 in Tlow (SD 19.7)), but remained at levels indicative of low stress. Overall ewe performance was impaired by the presence of trees, in terms of greater difficulty in regaining body weight and condition after weaning, although this varied between years. Lamb performance was not affected. The lower sward biomass (-50% on average between Tlow and Thigh) probably played a major role, and was not compensated by improved sward quality. Future research will help to identify appropriate tree arrangements and pasture management to best balance these positive and negative effects at the animal and plot level.
Section: Mathematical & Computational Biology ; Topics: Ecology, Statistics

Proper account of auto-correlations improves decoding performances of state-space (semi) Markov models

Bez, Nicolas; Gloaguen, Pierre; Etienne, Marie-Pierre; Lanco, Sophie; Joo, Rocío; Rivot, Etienne; Walker, Emily; Woillez, Mathieu; Mahévas, Stéphanie

10.24072/pcjournal.535 - Peer Community Journal, Volume 5 (2025), article no. e38.
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State-space models are widely used in ecology to infer hidden behaviors. This study develops an extensive numerical simulation-estimation experiment to evaluate the state decoding accuracy of four simple state-space models. These models are obtained by combining different Markovian specifications (Markov and semi-Markov) for the hidden layer with the absence (model AR0) and presence (AR1) of auto-correlation for the observation layer. Model parameters are issued from two sets of real annotated trajectories. Three metrics are developed to help interpret model performance. The first is the Hellinger distance between Markov and semi-Markov sojourn time probability distributions. The second is sensitive to the overlap between the probability density functions of state-dependent variables (e.g., speed variables). The third quantifies the deterioration of the inference conditions between AR0 and AR1 formulations. It emerges that the most sensitive model choice concerns the auto-correlation of the random processes describing the state-dependent variables. Opting for the absence of auto-correlation in the model while the state-dependent variables are actually auto-correlated, is detrimental to state decoding performance. Regarding the hidden layer, imposing a Markov structure while the state process is semi-Markov (with negative Binomial sojourn times) does not impair the state decoding performances. The real-life estimates are consistent with our experimental finding that performance deteriorates when there are significant temporal correlations that are not accounted for in the model. In light of these findings, we recommend that researchers carefully consider the structure of the statistical model they suggest and confirm its alignment with the process being modeled, especially when considering the auto-correlation of observed variables.
Section: Ecology ; Topics: Ecology, Environmental sciences, Evolution

Code-sharing policies are associated with increased reproducibility potential of ecological findings

Sánchez-Tójar, Alfredo; Bezine, Aya; Purgar, Marija; Culina, Antica

10.24072/pcjournal.541 - Peer Community Journal, Volume 5 (2025), article no. e37.
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Software code (e.g., analytical code) is increasingly recognised as an important research output because it improves transparency, collaboration, and research credibility. Many scientific journals have introduced code-sharing policies; however, surveys have shown alarmingly low compliance with these policies. In this study, we expanded on a recent survey of ecological journals with code-sharing policies by investigating sharing practices in a comparable set of ecological journals without code-sharing policies. Our aims were to estimate code- and data-sharing rates, assess key reproducibility-boosting features, such as the reporting of software versioning, and compare reproducibility potential between journals with and without a code-sharing policy. We reviewed a random sample of 314 articles published between 2015 and 2019 in 12 ecological journals without a code-sharing policy. Only 15 articles (4.8%) provided analytical code, with the percentage nearly tripling over time (2015-2016:2.5%, 2018-2019:7.0%). Data-sharing was higher than code-sharing (2015-2016:31.0%, 2018-2019:43.3%), yet only eight articles (2.5%) shared both code and data. Compared to a comparative sample of 346 articles from 14 ecological journals with a code-sharing policy, journals without a code-sharing policy showed 5.6 times lower code-sharing, 2.1 times lower data-sharing, and 8.1 times lower reproducibility potential. Despite these differences, the key reproducibility-boosting features of the two journal types were similar. Approximately 90% of all articles reported the analytical software used; however, for journals with and without a code-sharing policy, the software version was often missing (49.8% and 36.1% of articles, respectively), and exclusively proprietary (i.e., non-free) software was used in 16.7% and 23.5% of articles, respectively. Our study suggests that journals with a code-sharing policy have greater reproducibility potential than those without. Code-sharing policies are likely to be a necessary but insufficient step towards increasing reproducibility. Journals should prioritize adopting explicit, easy-to-find, and strict code-sharing policies to facilitate researchers' compliance and should implement mechanisms such as checklists to ensure adherence.
Section: Evolutionary Biology ; Topics: Evolution, Genetics/genomics, Population biology

Unraveling genetic load dynamics during biological invasion: insights from two invasive insect species

Lombaert, Eric; Blin, Aurélie; Porro, Barbara; Guillemaud, Thomas; Bernal, Julio S.; Chang, Gary; Kirichenko, Natalia; Sappington, Thomas W.; Toepfer, Stefan; Deleury, Emeline

10.24072/pcjournal.539 - Peer Community Journal, Volume 5 (2025), article no. e36.
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Many invasive species undergo a significant reduction in genetic diversity, i.e. a genetic bottleneck, in the early stages of invasion. However, this reduction does not necessarily prevent them from achieving considerable ecological success and becoming highly efficient colonizers. Here we investigated the purge hypothesis, which suggests that demographic bottlenecks may facilitate conditions (e.g., increased homozygosity and inbreeding) under which natural selection can purge deleterious mutations, thereby reducing genetic load. We used a transcriptome-based exome capture protocol to identify thousands of SNPs in coding regions of native and invasive populations of two highly successful invasive insect species, the western corn rootworm (Chrysomelidae: Diabrotica virgifera virgifera) and the harlequin ladybird (Coccinelidae: Harmonia axyridis). We categorized and polarized SNPs to investigate changes in genetic load between invasive populations and their sources. Our results differed between species. In D. virgifera virgifera, although there was a general reduction in genetic diversity in invasive populations, including that associated with genetic load, we found no clear evidence for purging of genetic load, except marginally for highly deleterious mutations in one European population. Conversely, in H. axyridis, the reduction in genetic diversity was minimal, and we detected signs of genetic load fixation in invasive populations. These findings provide new insights into the evolution of genetic load during invasions, but do not offer a definitive answer to the purge hypothesis. Future research should include larger genomic datasets and a broader range of invasive species to further elucidate these dynamics.

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The network image was drawn by Martin Grandjean: A force-based network visualization CC BY-SA