Latest Articles

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  Section: Evolutionary Biology ; Topics: Evolution, Computer sciences

  Rehabilitating the benefits of gene tree correction in the presence of incomplete lineage sorting

  Lafond, Manuel;   Scornavacca, Celine  

  10.24072/pcjournal.674 - Peer Community Journal, Volume 6 (2026), article no. e7

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  Gene trees play an important role in various areas of phylogenomics. However, their reconstruction often relies on limited-length sequences and may not account for complex evolutionary events, such as gene duplications, losses, or incomplete lineage sorting (ILS), which are not modeled by standard phylogenetic methods. To address these challenges, it is common to first infer gene trees using fast algorithms for conventional models, then refine them through species tree-aware correction methods. Recently, it has been argued that such corrections can lead to overfitting and force gene trees to resemble the species tree, thereby obscuring genuine gene-level variation caused by ILS. In this paper, we challenge and refute this hypothesis, and we demonstrate that, when applied carefully, correction methods can offer significant benefits, even in the presence of ILS.

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  Section: Zoology ; Topics: Genetics/genomics

  Nanopore genome skimming with Illumina polishing yields highly accurate mitogenome sequences: a case study of Niphargus amphipods

  Salussolia, Alice;   Lecoquierre, Ninon; Stoch, Fabio;   Flot, Jean-François  

  10.24072/pcjournal.671 - Peer Community Journal, Volume 6 (2026), article no. e6

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  With over 430 species currently described, the amphipod genus Niphargus Schiödte, 1849 is the most species-rich crustacean genus in subterranean waters. Previous phylogenetic studies of this genus have relied mainly on mitochondrial COI and nuclear 28S sequences, which do not resolve all the nodes in its phylogeny. As a first step towards a mitogenome-based phylogeny of niphargids, we present here the first complete mitogenome sequence of Niphargus. To obtain high-accuracy mitogenome sequences and annotations, genome skimming of three individuals of Niphargus dolenianensis Lorenzi, 1898 was performed using both short, accurate reads (Illumina) and long, noisier reads (nanopore). Whereas the direct assembly of Illumina sequences yielded structurally incorrect mitogenome sequences, the assembly of nanopore reads produced highly accurate sequences that were corroborated by the mapping of Illumina reads. Polishing the nanopore consensus using Illumina reads corrected a handful of errors at the homopolymer level. The resulting mitogenome sequences ranged from 14,956 to 15,199 bp and shared the same arrangement of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a putative control region. Phylogenetic analyses based on protein-coding genes confirmed that the Niphargidae family is sister to Pseudoniphargidae, resolving their relationships with other amphipod families. This highlights the utility of mtDNA genome sequences for studying the evolution of this groundwater genus, and the refinement of new methodological approaches, such as nanopore sequencing, is promising for the study of its origin and diversification.

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  Section: Forest & Wood Sciences ; Topics: Applied biological sciences, Environmental sciences, Plant biology

  Comparative responses of legume vs. non-legume tropical trees to biochar additions

  Thomas, Sean C.;   Halim, M. A.;   Ali, Syed Tuhin  

  10.24072/pcjournal.668 - Peer Community Journal, Volume 6 (2026), article no. e5

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  Nitrogen-fixing plants in the legume family (Fabaceae) may show particularly large positive responses to biochar additions due to their capacity to potentially compensate for reduced N in biochar-amended soils. Prior studies also suggest that biochar may have specific developmental effects on legumes, including increased root nodulation and altered morphology. We examined the growth and morphometric responses of legume and non-legume tropical trees to biochar additions in a common garden pot trial experiment. Four legume species (Acacia auriculiformis, A. mangium, Delonix regia, and Pterocarpus santalinus) and four non-legumes (Eucalyptus alba, Melia azedarach, Swietenia macrophylla, and Syzygium cumini) were compared in terms of sapling responses to additions of a wood-feedstock biochar applied at 10 and 20 t/ha. Overall, strong positive effects of biochar additions on sapling performance were observed, with an average increase of 30% in total biomass and a notable increase in height relative to diameter growth. Species showed pronounced differences in responses, with strong interactive effects of species and biochar treatments on growth metrics. Legume species showed an average increase somewhat greater than non-legumes; however, responses were variable among species, with the two Acacia species showing the largest responses, resulting in a non-significant pattern. A literature-based meta-analysis of tropical and subtropical trees likewise suggests greater biochar responses in legumes, but the analysis also falls short of statistical significance. In addition, experimental results indicate large interactive effects of species and biochar on soil pH and other soil properties. Large growth responses of certain taxa of legumes (and other taxa) to biochar, and pronounced species-specific effects on soil properties, may reflect evolved responses to fire disturbance that can be leveraged in the context of forest restoration and enhanced carbon sequestration in degraded tropical landscapes.

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  Section: Health & Movement Sciences ; Topics: Psychological and cognitive sciences, Health sciences, Neuroscience

  Comparison of two exergame-based motor-cognitive trainings: protocol for a pilot study on cognitive, motor, and psychiatric symptoms in patients with Huntington’s disease (CARE-MH)

  Godard, Julien;   Chartier, Coline;   Besnard, Jérémy;   Allain, Philippe;   Humeau-Heurtier, Anne;   Durand, Sylvain  

  10.24072/pcjournal.676 - Peer Community Journal, Volume 6 (2026), article no. e4

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  Background: Huntington’s disease (HD) is a rare, hereditary neurodegenerative disorder. Symptoms manifest around the age of 40 and encompass a range of physical, cognitive, and psychiatric impairments. Motor and cognitive exercises have been shown to slow the progression of symptoms. Particular attention has been given to motor-cognitive training, which may combine the benefits and contribute to delaying the progression of the disease. However, studies investigating the efficacy of such training in HD remain limited. At the same time, the use of exergaming has shown promise in improving participant engagement in training, which may in turn enhance both physical and cognitive functioning. The aim of our pilot study is to evaluate the feasibility and effects of two home-based motor-cognitive trainings via an exergame on motor, cognitive, and psychiatric symptomatology in HD patients. Methods: Patients, from stages 1 and 2, will be randomly assigned to one of the two groups: sequential exercises (separate motor and cognitive exercises) or synergical exercises (simultaneous motor and cognitive exercises). Training sessions will be conducted individually over a 12-week period (3 sessions/week ; 60 minutes/session). Linear mixed-effects models will be used to assess training’s effects on balance, walking capacity, lower-extremity strength, disease-related motor impairments, global cognition, executive functions, depression, anxiety, disease-specific psychiatric symptoms, and quality of life. Discussion: Our pilot study will be the first one to compare two exergame-based motor-cognitive trainings in HD patients. It is expected to be feasible, with improvements in motor, cognitive, and psychiatric symptoms in both groups. However, greater improvements are expected in the synergical group compared to the sequential group.