Latest Articles

Section: Ecology ; Topics: Ecology, Environmental sciences, Population biology

Long term trend and short-term dynamics of a willow ptarmigan population

Willebrand, Tomas; Hörnell-Willebrand, Maria; Brittas, Rolf; Kleiven, Eivind Flittie

10.24072/pcjournal.590 - Peer Community Journal, Volume 5 (2025), article no. e98
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Willow ptarmigan Lagopus lagopus is abundant in Arctic and tundra regions, but rapid climate warming has raised concerns about possible declines as has been observed in several bird species. In this study, we used a hierarchical state-space model to analyze data from a 139 km line transects in mid-Sweden over 48 years. Adult numbers and breeding success were analyzed separately, and we included covariates on vole abundance, numbers of snow-free days in autumn and spring, and the last day of frost in May. We assessed long-term trends in the adult population and estimated the effects of breeding success and weather variation on short-term changes. The estimates of adult density did not show any trend for the period 1976 to 2023, and the dynamics were characterized by a strong direct negative density dependence indicating a stationary process. A number of possible mechanisms have been suggested for how a warmer climate affects willow ptarmigan population dynamics, but our results do not support the hypothesis that lack of snow in autumn and spring increases the vulnerability of willow ptarmigan to predation and leads to population decline. Breeding success is an important driver of changes in, but independent of, adult density. In addition to predation, we propose that climate conditions and emerging vegetation during egg formation and laying are important. We suggest that our results can be explained by a diverse predator assemblage that makes it difficult for the population to escape top-down control, resulting in short-term fluctuations at lower densities.
Section: Evolutionary Biology ; Topics: Evolution, Genetics/genomics

Population structure and genetic diversity of the Critically Endangered bowmouth guitarfish (Rhina ancylostomus) in the Northwest Indian Ocean

Kipperman, Marja J.; Jabado, Rima W.; Haque, Alifa Bintha; Fernando, Daniel; Anjani, P.A.D.L; Spaet, Julia L.Y.; Humble, Emily

10.24072/pcjournal.623 - Peer Community Journal, Volume 5 (2025), article no. e97
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The bowmouth guitarfish (Rhina ancylostomus) is a unique and understudied species of wedgefish with a distribution spanning the Indo-Pacific Oceans. Due to targeted and bycatch fisheries, this species is experiencing serious declines across its range. It is now considered among the most threatened species of elasmobranch. Despite this, species-specific management is limited, particularly around primary fishing hotspots. This is in part due to knowing very little about fundamental population processes. Here, we combine mitochondrial and single nucleotide polymorphism (SNP) data to carry out the first genetic assessment of R. ancylostomus across the Northwest Indian Ocean. We detect genetic differentiation across the northwest range, shaped by both oceanographic barriers and intrinsic dispersal constraints, and uncover a cline in genetic variation from east to west. These findings emphasise the importance of maintaining habitat connectivity while also identifying regions that may require heightened protection. In doing so, our study provides a critical baseline for conservation planning of R. ancylostomus and highlights the value of genomic data in elasmobranch conservation.
Section: Evolutionary Biology ; Topics: Evolution

Integrating ethnolinguistic and archaeobotanical data to uncover the origin and dispersal of cultivated sorghum in Africa: a genomic perspective

Gilabert, Aude; Deu, Monique; Champion, Louis; Cubry, Philippe; Donkpegan, Armel; Rami, Jean-Francois; Pot, David; Vigouroux, Yves; Leclerc, Christian

10.24072/pcjournal.613 - Peer Community Journal, Volume 5 (2025), article no. e96
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Archaeobotanical evidence suggests that the beginning of cultivation and emergence of domesticated sorghum was located in eastern Sudan during the fourth millennium BCE. Here, we used a genomic approach, together with archaeobotanical and ethnolinguistic data, to refine the spatial and temporal origin and the spread of cultivated sorghum in Africa. We built a probability map of the origin of sorghum domestication in Eastern Africa using genomic data and spatial Bayesian models. The origin was located in Eastern Sudan and Western Ethiopia, in perfect concordance with recent archaeobotanical evidence. Calibrated on archaeological remains, our genomic-based model suggests that the beginning of the expansion of sorghum agriculture took place around 4,600 years ago. Spread of sorghum cultivation led to a sorghum population structure fitting ethnolinguistic groups at different scales, suggesting that human social groups and sorghum populations co-diffused. Consequently, ethnolinguistic barriers and social preferences, as well as adaptation to specific climate zones, have contributed to structuring domesticated sorghum diversity during its diffusion.
Section: Evolutionary Biology ; Topics: Evolution, Genetics/genomics, Population biology

Performance evaluation of adaptive introgression classification methods

Romieu, Jules; Camarata, Ghislain; Crochet, Pierre-André; de Navascués, Miguel; Leblois, Raphaël; Rousset, François

10.24072/pcjournal.617 - Peer Community Journal, Volume 5 (2025), article no. e95
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Introgression, the incorporation of foreign variants through hybridization and repeated backcross, is increasingly being studied for its potential evolutionary consequences, one of which is adaptive introgression (AI). In recent years, several statistical methods have been proposed for the detection of loci that have undergone adaptive introgression. Most of these methods have been tested and developed to infer the presence of Neanderthal or Denisovan AI in humans. Currently, the behaviour of these methods when faced with genomic datasets from evolutionary scenarios other than the human lineage remains unknown. This study therefore focuses on testing the performance of the methods using test data sets simulated under various evolutionary scenarios inspired by the evolutionary history of human, wall lizard (Podarcis) and bear (Ursus) lineages. These lineages were chosen to represent different combinations of divergence and migration times. We study the impact of these parameters, as well as migration rate, population size, selection coefficient and presence of recombination hotspots, on the performance of three methods (VolcanoFinder, Genomatnn and MaLAdapt) and a standalone summary statistic (Q95(w, y)). Furthermore, the hitchhiking effect of an adaptively introgressed mutation can have a strong impact on the flanking regions, and therefore on the discrimination between the genomic windows classes (i.e. AI/non-AI). For this reason, three different types of non-AI windows are taken into account in our analyses: independently simulated neutral introgression windows, windows adjacent to the window under AI, and windows coming from a second neutral chromosome unlinked to the chromosome under AI. Our results highlight the importance of taking into account adjacent windows in the training data in order to correctly identify the window with the mutation under AI. Finally, our tests show that methods based on Q95 seem to be the most efficient for an exploratory study of AI.

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