Latest Articles

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  Section: Evolutionary Biology ; Topics: Evolution, Genetics/genomics

  Limited directional selection but coevolutionary signals among imprinted genes in A. lyrata

  Le veve, Audrey;   Iltas, Ömer;   Dutheil, Julien;   Lafon Placette, Clement  

  10.24072/pcjournal.702 - Peer Community Journal, Volume 6 (2026), article no. e26

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  Genomic imprinting is a form of gene regulation leading to the unequal expression of maternal and paternal alleles. The main hypothesis invoked to explain the evolution of imprinted genes is the kinship theory, which posits a conflict between parental genomes over resource allocation in progeny. According to this theory, such conflicts select for parent-of-origin–dependent expression of genes involved in resource allocation. How such conflicts translate into signatures of selection at coding or regulatory sequences remains model-dependent and is not explicitly predicted by the kinship theory. However, most studies addressing selection in imprinted genes in flowering plants, particularly those based on population-genomic or phylogenetic analyses, have focused on self-fertilizing species, where conflicts over resource allocation are predicted to be weak. Consequently, the impact of the kinship theory on the evolution of imprinted genes remains largely unexplored in systems where parental conflict is expected to be strong. Furthermore, potential coevolution between antagonistically acting imprinted genes, as proposed in extensions of parental conflict models, has not yet been tested empirically. Using combined phylogenetic and population genomic approaches, we investigated signatures of selection on imprinted genes across the Brassicaceae family and in autogamous and allogamous populations of Arabidopsis lyrata, and searched for evidence of coevolution among imprinted genes. We found that endosperm-expressed genes exhibited signals of balancing selection across Brassicaceae and within allogamous populations, consistent with models of unresolved intralocus conflict. These population-level signals varied with the mating system, in line with expectations that parental conflict is reduced under self-fertilization. Moreover, phylogenetic analyses indicated signatures of purifying (negative) selection acting on imprinted genes. However, the population-level signatures of selection were independent of the mating system and showed limited concordance with kinship predictions, possibly due to stronger selection acting on expression than on coding sequences. Finally, we identified coevolution between imprinted genes, although not at specific sites, suggesting that interactions beyond protein sequence may contribute to this process.

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  Section: Evolutionary Biology ; Topics: Evolution

  The effect of gene tree dependence on summary methods for species tree inference

  He, Wanting;   Scornavacca, Celine;   Chan, Yao-ban  

  10.24072/pcjournal.694 - Peer Community Journal, Volume 6 (2026), article no. e25

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  When inferring the evolutionary history of species and the genes they contain, the phylogenetic trees of genes can be different from those of the species and to each other, due to a variety of causes, including incomplete lineage sorting. We often wish to infer the species tree, but only reconstruct the gene trees from sequences. We then combine the gene trees to produce a species tree; methods to do this are known as summary methods, of which ASTRAL is currently among the most popular. ASTRAL has been shown to be accurate in many practical scenarios through extensive simulations. However, these simulations generally assume that the input gene trees are independent of each other (infinite recombination between loci). This is known to be unrealistic, as genes that are close to each other on the chromosome (or are co-evolving) have dependent phylogenies. In this paper, we develop a model for generating dependent gene trees within a species tree, based on the coalescent with recombination. We then use these trees as input to ASTRAL to reassess its accuracy for dependent gene trees. Our results allow us to evaluate the impact of any level of dependence on the accuracy of ASTRAL, both when gene trees are known and estimated from sequences. We find that a fixed amount of dependence reduces the effective sample size by a constant factor. In current phylogenomic datasets, loci are generally sampled at large genomic distances to reduce gene tree dependence, thereby limiting the number of genes available for inference. However, full independence between genes is not required for accurate species tree estimation, and excluding gene trees may reduce inference accuracy. This creates a trade-off between the number of genes used and the degree of gene tree dependence. We therefore propose a method to identify the minimum genomic separation required to maintain satisfactory inference accuracy.

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  Section: Ecology ; Topics: Ecology, Evolution

  Infanticide in a colonial cooperative bird is not associated with direct reproductive benefits

  Covas, Rita;   Silva, Liliana R.;   Ferreira, André C.;   D’Amelio, Pietro B.;   Fortuna, Rita;   Duval, Delphine;   Paquet, Matthieu;   Doutrelant, Claire  

  10.24072/pcjournal.700 - Peer Community Journal, Volume 6 (2026), article no. e24

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  Infanticide, the killing of dependent young by adult conspecifics, is an extreme form of conflict that remains poorly understood. Previous studies suggest that it is associated with reproductive benefits, either by making breeders newly available for reproduction or by increasing offspring care and reducing competition for resources. In addition, infanticide may result from a reproductive trade-off, where parents kill their offspring if environmental conditions compromise their reproductive value. Here, we combine video, genetic and individual-level reproductive data collected over 12 years to describe infanticide in a highly social, cooperative bird, the sociable weaver Philetairus socius and to establish whether direct reproductive benefits or life-history trade-offs are possible motivators for this behaviour. We documented 50 cases of infanticide and identified 27 aggressors with known histories. These were mostly born outside the colonies where they committed infanticide (63%) and there was a bias towards younger individuals. Aggressors were usually not part of the victim’s breeding group (74%), but in two cases infanticide was committed by the breeding female, and in five by helpers. In most cases, aggressors were not reproducing at the time of the infanticide, were not recorded mating with any of the breeders or helpers from the attacked nest, nor occupied the nest from where the chicks were evicted. Only 13 of the known aggressors were confirmed as breeders after the attacks, and these mostly reproduced at the colony where the attacks were committed. Overall, we found no evidence for direct reproductive benefits of infanticide in sociable weavers. However, the younger age of aggressors, lack of genetic relatedness to the victims and future breeding at the colony suggest that competition between breeding groups, and hence indirect reproductive benefits, could provide motivation for infanticide in this population. Additional work over longer periods is needed to identify these possible indirect fitness benefits of infanticide.

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  Section: Animal Science ; Topics: Agricultural sciences, Physiology

  Evolution of voluntary intake by dairy cows during the dry period

  Huang, Yayu;   Oble, Lucile; Jurquet, Julien; Delaby, Luc

  10.24072/pcjournal.695 - Peer Community Journal, Volume 6 (2026), article no. e23

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  Dairy cow’s feeding during the dry period is an essential step in ensuring that the next lactation runs smoothly. It has been demonstrated that feeding the dry cows ad libitum with low energy, high fill value diet apears to be beneficial. However, the voluntary intake of dry cows has received little attention. Existing prediction model for intake capacity may fail to capture the specific characteristics of dry cows, particularly regarding their milk yield potential. We conducted this study to evaluate the volutary intake of dairy cows receiving a TMR with high fill value, assess it’s variability depending on cow’s characteristic and adjust the INRA prediction models of intake capacity of dairy cows during the dry period. Sixty-two Holstein cows were enrolled in the experiment which carried out during 3 consecutive years. The dry-off took place 8 weeks before the expected parturition. After a 1-week transition period, cows were fed a total mixed ration (TMR) until calving (the last 6 weeks were considered for analysis). Dry matter intake (DMI) averaged 16.9 kg, it declined from 17.4 kg at week - 6 to 15.9 kg at week - 1 (p < 0.001). Parity (p < 0.001), BCS (p < 0.001), body weight (p < 0.05), week relative to parturition (p < 0.001) and peak milk yield potential of the ended lactation (p < 0.01) significantly influenced DMI. Depending on these results, the INRA model for prediction of intake capacity of pregnant dry cows has been revised and adjusted. Additional measured data on DMI in dry cows under various experimental conditions, such as different diet compositions or varying durations of the dry period, would be requied to confirm the consistency of the new IC prediction model and to refine a more representative coefficient before proposing the final adjusted equation.