Latest Articles

Section: Genomics ; Topics: Agricultural sciences, Genetics/genomics, Population biology

Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds

Bortoluzzi, Chiara; Restoux, Gwendal; Rouger, Romuald; Desnoues, Benoit; Petitjean, Florence; Bosse, Mirte; Tixier-Boichard, Michèle

10.24072/pcjournal.474 - Peer Community Journal, Volume 4 (2024), article no. e99.
Get full text PDF

Livestock biodiversity is declining globally at rates unprecedented in human history. Of all avian species, chickens are among the most affected ones because many local breeds have a small effective population size that makes them more susceptible to demographic and genetic stochasticity. The maintenance of genetic diversity and control over genetic drift and inbreeding by conservation programs are fundamental to ensure the long-term survival and adaptive potential of a breed. However, while the benefits of a conservation program are well understood, they are often overlooked. We here used temporal whole-genome sequencing data to assess the effects of a conservation program on the genetic diversity (Δπ), deleterious variation (ΔL), and inbreeding (ΔF) of two local French chicken breeds, the Barbezieux and Gasconne. We showed that when the conservation program is consistent over time and does not undergo any major organisational changes (i.e., Barbezieux), the loss of genetic diversity is limited. This was true for both pedigree and genomic inbreeding but also for the genetic load estimated from functionally important genome-wide variants. However, when a conservation program is interrupted or re-initiated from scratch (i.e., Gasconne), the loss of genetic diversity can hardly be limited as a result of the bottleneck effect associated with the re-sampling. Our results reinforce the imperative to establish and sustain existing conservation programs that aim to keep populations with a relatively small effective population size from the brink of extinction. Moreover, we conclude by encouraging the use of molecular data to more effectively monitor inbreeding at the genome level while improving fitness by tracking protein-coding and non-coding deleterious variants.
Section: Ecology ; Topics: Ecology

Body mass change over winter is consistently sex-specific across roe deer (Capreolus capreolus) populations

Hewison, A.J. Mark; Bonnot, Nadège C.; Gaillard, Jean-Michel; Kjellander, Petter; Lemaitre, Jean-François; Morellet, Nicolas; Pellerin, Maryline

10.24072/pcjournal.479 - Peer Community Journal, Volume 4 (2024), article no. e98.
Get full text PDF

In most polygynous vertebrates, males must allocate energy to growing secondary sexual characteristics, such as ornaments or weapons, that they require to attract and defend potential mates, impacting body condition and potentially entailing fitness costs. We investigated sex differences in over winter body mass change across five intensively monitored populations of roe deer (Capreolus capreolus) with markedly contrasting environmental conditions. At winter onset, males weighed, on average, 8.4% (from 4.7% in the most northerly population to 11.6% in the most southerly one) more than females. However, across all populations, males fared worse over the winter than females, losing more (Sweden) or gaining less (France) mass, so that sexual mass dimorphism was virtually absent prior to the onset of spring. Our findings reveal that the direction of over-winter change in mass of roe deer depends on winter severity, but that males are consistently more sensitive to this environmental constraint than females. As a result of this sex-specific change in body mass, sexual mass dimorphism is lowest at the onset of the territorial season. We suggest that allocation to antler growth and territory establishment drives this pattern, providing a likely explanation to account for the lower rates of male adult survival that are consistently reported in this weakly dimorphic species.
Section: Ecology ; Topics: Ecology, Environmental sciences

InsectChange: Comment

Gaume, Laurence; Desquilbet, Marion

10.24072/pcjournal.469 - Peer Community Journal, Volume 4 (2024), article no. e97.
Get full text PDF

The InsectChange database (van Klink et al. 2021) underlying the meta-analysis by van Klink et al. (2020a) compiles worldwide time series of the abundance and biomass of invertebrates reported as insects and arachnids, as well as ecological data likely to have influenced the observed trends. On the basis of a comprehensive review of the original studies, we highlight numerous issues in this database, such as errors in insect counts, sampling biases, inclusion of noninsects driving assemblage trends, omission of drivers investigated in original studies and inaccurate assessment of local cropland cover. We show that in more than half of the original studies, the factors investigated were experimentally manipulated or were strong -often not natural- disturbances. These internal drivers created situations more frequently favouring an increase than a decrease in insects and were unlikely to be representative of habitat conditions worldwide. We demonstrate that when both groups were available in original freshwater studies, selecting all invertebrates rather than only insects led to an overestimation of the “insect” trend. We argue that the disparate and non-standardised units of measurement of insect density among studies may have detrimental consequences for users, as was the case for van Klink et al. (2020a, 2022) who log₁₀(x+1)-transformed these heterogeneous data, compromising the comparison of temporal trends between datasets and the estimation of the overall trend. We show that geographical coordinates assigned by InsectChange to insect sampling areas are inadequate for the analysis of the local influence of agriculture, urbanisation and climate on insect change for 68% of the datasets. In terrestrial data, the local cropland cover is strongly overestimated, which may incorrectly dismiss agriculture as a driving force behind the decline in insects. Therefore, in its current state, this database enables the study of neither the temporal trends of insects worldwide nor their drivers. The supplementary information accompanying our paper presents in detail each problem identified and makes numerous suggestions that can be used as a basis for improvement.
Section: Mathematical & Computational Biology ; Topics: Biophysics and computational biology

HairSplitter: haplotype assembly from long, noisy reads

Faure, Roland; Lavenier, Dominique; Flot, Jean-François

10.24072/pcjournal.481 - Peer Community Journal, Volume 4 (2024), article no. e96.
Get full text PDF

Motivation: Long-read assemblers face challenges in discerning closely related viral or bacterial strains, often collapsing similar strains into a single sequence. This limitation has been hampering metagenome analysis, as diverse strains may harbor crucial functional distinctions. Results: We introduce a novel software, HairSplitter, designed to retrieve strains from a partially or totally collapsed assembly and long reads. The method uses a custom variant-calling process to operate with erroneous long reads and introduces a new read binning algorithm to recover an a priori unknown number of strains. On noisy long reads, HairSplitter recovers more strains while being faster than state-of-the-art tools, both in the cases of viruses and bacteria. Availability: HairSplitter is freely available on GitHub at https://github.com/RolandFaure/Hairsplitter (https://doi.org/10.5281/zenodo.13753481).

View more articles

Follow us

People

Sections

Conferences

Euring 2023

Indexed by

View all databases

Supporters

View all supporters

Membership

View all membership

Image Credits

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