Unravelling the maternal evolutionary history of the African leopard (Panthera pardus pardus).

The African leopard (Panthera pardus pardus) has lost a significant proportion of its historical range, notably in north-western Africa and South Africa. Recent studies have explored the genetic diversity and population structure of African leopards across the continent. A notable genetic observation is the presence of two divergent mitochondrial lineages, PAR-I and PAR-II. Both lineages appeared to be distributed widely, with PAR-II frequently found in southern Africa. Until now, no study has attempted to date the emergence of either lineage, assess haplotype distribution, or explore their evolutionary histories in any detail. To investigate these underappreciated questions, we compiled the largest and most geographically representative leopard data set of the mitochondrial NADH-5 gene to date. We combined samples (n = 33) collected in an altitudinal transect across the Mpumalanga province of South Africa, where two populations of leopard are known to be in genetic contact, with previously published sequences of African leopard (n = 211). We estimate that the maternal PAR-I and PAR-II lineages diverged approximately 0.7051 (0.4477-0.9632) million years ago (Ma). Through spatial and demographic analyses, we show that while PAR-I underwent a mid-Pleistocene population expansion resulting in several closely related haplotypes with little geographic structure across much of its range, PAR-II remained at constant size and may even have declined slightly in the last 0.1 Ma. The higher genetic drift experienced within PAR-II drove a greater degree of structure with little haplotype sharing and unique haplotypes in central Africa, the Cape, KwaZulu-Natal and the South African Highveld. The phylogeographic structure of PAR-II, with its increasing frequency southward and its exclusive occurrence in south-eastern South Africa, suggests that this lineage may have been isolated in South Africa during the mid-Pleistocene. This hypothesis is supported by historical changes in paleoclimate that promoted intense aridification around the Limpopo Basin between 1.0-0.6 Ma, potentially reducing gene flow and promoting genetic drift. Interestingly, we ascertained that the two nuclear DNA populations identified by a previous study as East and West Mpumalanga correspond to PAR-I and PAR-II, respectively, and that they have come into secondary contact in the Lowveld region of South Africa. Our results suggest a subdivision of African leopard mtDNA into two clades, with one occurring almost exclusively in South Africa, and we identify the potential environmental drivers of this observed structure. We caution that our results are based on a single mtDNA locus, but it nevertheless provides a hypothesis that can be further tested with a dense sample of nuclear DNA data, preferably whole genomes. If our interpretation holds true, it would provide the first genetic explanation for the smaller observed size of leopards at the southernmost end of their range in Africa.

Characterisation of the mitochondrial genome and phylogenetic analysis of Toxocara apodemi (Nematoda: Ascarididae).

We first sequenced and characterised the complete mitochondrial genome of Toxocara apodeme, then studied the evolutionary relationship of the species within Toxocaridae. The complete mitochondrial genome was amplified using PCR with 14 specific primers. The mitogenome length was 14303 bp in size, including 12 PCGs (encoding 3,423 amino acids), 22 tRNAs, 2 rRNAs, and 2 NCRs, with 68.38% A+T contents. The mt genomes of T. apodemi had relatively compact structures with 11 intergenic spacers and 5 overlaps. Comparative analyses of the nucleotide sequences of complete mt genomes showed that T. apodemi had higher identities with T. canis than other congeners. A sliding window analysis of 12 PCGs among 5 Toxocara species indicated that nad4 had the highest sequence divergence, and cox1 was the least variable gene. Relative synonymous codon usage showed that UUG, ACU, CCU, CGU, and UCU most frequently occurred in the complete genomes of T. apodemi. The Ka/Ks ratio showed that all Toxocara mt genes were subject to purification selection. The largest genetic distance between T. apodemi and the other 4 congeneric species was found in nad2, and the smallest was found in cox2. Phylogenetic analyses based on the concatenated amino acid sequences of 12 PCGs demonstrated that T. apodemi formed a distinct branch and was always a sister taxon to other congeneric species. The present study determined the complete mt genome sequences of T. apodemi, which provide novel genetic markers for further studies of the taxonomy, population genetics, and systematics of the Toxocaridae nematodes.

Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus in Xinjiang, China, from 2020 to 2022.

In recent years, the pig industry in Xinjiang, China, has been severely impacted by outbreaks of porcine epidemic diarrhea (PED), despite vaccination efforts. In this study, we investigated the genetic characteristics of currently prevalent porcine epidemic diarrhea virus (PEDV) strains in the region. We collected 548 samples from animals with suspected PED on large-scale pig farms in Xinjiang. Of these, 258 tested positive for PEDV by RT-PCR, yielding an overall positivity rate of 47.08%. S1 gene sequencing and phylogenetic analysis were conducted on 23 randomly selected RT-PCR-positive samples. Three endemic strains of PEDV (PEDV/CH/XU/2020, PEDV/CH/XK/2020, and PEDV/CH/XA/2020) were isolated, and their complete genome sequences were analyzed for evidence of genetic recombination. Sequence comparison of the S gene indicated significant variations in the S1 gene of the Xinjiang strains compared to the vaccine strains CV777, AJ1102, and LWL, with 90.2%-98.5% nucleotide sequence identity. Notably, both the N-terminal and C-terminal domains of the S protein showed significant variation. Genetic evolutionary analysis identified the GIIa subtype as the dominant genotype among the epidemic strains in Xinjiang. Recombination analysis revealed inter-subtype recombination events in the PEDV/CH/XK/2020 and XJ1904-34 strains. These findings highlight the extensive genetic variation in the predominant GIIa genotype of PEDV in Xinjiang, which does not match the genotype of the currently used vaccine strains. These data may guide further efforts toward the development of effective vaccines for the control of PED.

Exploring the origin of a unique mutant allele in twin-tail goldfish using CRISPR/Cas9 mutants.

Artificial selection has been widely applied to genetically fix rare phenotypic features in ornamental domesticated animals. For many of these animals, the mutated loci and alleles underlying rare phenotypes are known. However, few studies have explored whether these rare genetic mutations might have been fixed due to competition among related mutated alleles or if the fixation occurred due to contingent stochastic events. Here, we performed genetic crossing with twin-tail ornamental goldfish and CRISPR/Cas9-mutated goldfish to investigate why only a single mutated allele-chdS with a E127X stop codon (also called chdAE127X)-gives rise to the twin-tail phenotype in the modern domesticated goldfish population. Two closely related chdS mutants were generated with CRISPR/Cas9 and compared with the E127X allele in F2 and F3 generations. Both of the CRISPR/Cas9-generated alleles were equivalent to the E127X allele in terms of penetrance/expressivity of the twin-tail phenotype and viability of carriers. These findings indicate that multiple truncating mutations could have produced viable twin-tail goldfish. Therefore, the absence of polymorphic alleles for the twin-tail phenotype in modern goldfish likely stems from stochastic elimination or a lack of competing alleles in the common ancestor. Our study is the first experimental comparison of a singular domestication-derived allele with CRISPR/Cas9-generated alleles to understand how genetic fixation of a unique genotype and phenotype may have occurred. Thus, our work may provide a conceptual framework for future investigations of rare evolutionary events in domesticated animals.

Morphological disparity and structural performance of the dromaeosaurid skull informs ecology and evolutionary history.

Non-avialan theropod dinosaurs had diverse ecologies and varied skull morphologies. Previous studies of theropod cranial morphology mostly focused on higher-level taxa or characteristics associated with herbivory. To better understand morphological disparity and function within carnivorous theropod families, here we focus on the Dromaeosauridae, 'raptors' traditionally seen as agile carnivorous hunters.We applied 2D geometric morphometrics to quantify skull shape, performed mechanical advantage analysis to assess the efficiency of bite force transfer, and performed finite element analysis to examine strain distribution in the skull during biting. We find that dromaeosaurid skull morphology was less disparate than most non-avialan theropod groups. Their skulls show a continuum of form between those that are tall and short and those that are flat and long. We hypothesise that this narrower morphological disparity indicates developmental constraint on skull shape, as observed in some mammalian families. Mechanical advantage indicates that Dromaeosaurus albertensis and Deinonychus antirrhopus were adapted for relatively high bite forces, while Halszkaraptor escuilliei was adapted for high bite speed, and other dromaeosaurids for intermediate bite forces and speeds. Finite element analysis indicates regions of high strain are consistent within dromaeosaurid families but differ between them. Average strain levels do not follow any phylogenetic pattern, possibly due to ecological convergence between distantly-related taxa.Combining our new morphofunctional data with a re-evaluation of previous evidence, we find piscivorous reconstructions of Halszkaraptor escuilliei to be unlikely, and instead suggest an invertivorous diet and possible adaptations for feeding in murky water or other low-visibility conditions. We support Deinonychus antirrhopus as being adapted for taking large vertebrate prey, but we find that its skull is relatively less resistant to bite forces than other dromaeosaurids. Given the recovery of high bite force resistance for Velociraptor mongoliensis, which is believed to have regularly engaged in scavenging behaviour, we suggest that higher bite force resistance in a dromaeosaurid taxon may reflect a greater reliance on scavenging rather than fresh kills.Comparisons to the troodontid Gobivenator mongoliensis suggest that a gracile rostrum like that of Velociraptor mongoliensis is ancestral to their closest common ancestor (Deinonychosauria) and the robust rostra of Dromaeosaurus albertensis and Deinonychus antirrhopus are a derived condition. Gobivenator mongoliensis also displays a higher jaw mechanical advantage and lower resistance to bite force than the examined dromaeosaurids, but given the hypothesised ecological divergence of troodontids from dromaeosaurids it is unclear which group, if either, represents the ancestral condition. Future work extending sampling to troodontids would therefore be invaluable and provide much needed context to the origin of skull form and function in early birds. This study illustrates how skull shape and functional metrics can discern non-avialan theropod ecology at lower taxonomic levels and identify variants of carnivorous feeding.

The axial skeleton of Tiktaalik roseae.

The axial columns of the earliest limbed vertebrates show distinct patterns of regionalization as compared to early tetrapodomorphs. Included among their novel features are sacral ribs, which provide linkage between the vertebral column and pelvis, contributing to body support and propulsion by the hindlimb. Data on the axial skeletons of the closest relatives of limbed vertebrates are sparce, with key features of specimens potentially covered by matrix. Therefore, it is unclear in what sequence and under what functional context specializations in the axial skeletons of tetrapods arose. Here, we describe the axial skeleton of the elpistostegalian Tiktaalik roseae and show that transformations to the axial column for head mobility, body support, and pelvic fin buttressing evolved in finned vertebrates prior to the origin of limbs. No atlas-axis complex is observed; however, an independent basioccipital-exoccipital complex suggests increased mobility at the occipital vertebral junction. While the construction of vertebrae in Tiktaalik is similar to early tetrapodomorphs, its ribs possess a specialized sacral domain. Sacral ribs are expanded and ventrally curved, indicating likely attachment to the expanded iliac blade of the pelvis by ligamentous connection. Thus, the origin of novel rib types preceded major alterations to trunk vertebrae, and linkage between pelvic fins and axial column preceded the origin of limbs. These data reveal an unexpected combination of post-cranial skeletal characters, informing hypotheses of body posture and movement in the closest relatives of limbed vertebrates.

Genome-Wide Identification and Expression Analysis of TGA Family Genes Associated with Abiotic Stress in Sunflowers (Helianthus annuus L.).

Sunflower (Helianthus annuus L.) is an important, substantial global oil crop with robust resilience to drought and salt stresses. The TGA (TGACG motif-binding factor) transcription factors, belonging to the basic region leucine zipper (bZIP) family, have been implicated in orchestrating multiple biological processes. Despite their functional significance, a comprehensive investigation of the TGA family's abiotic stress tolerance in sunflowers remains elusive. In the present study, we identified 14 TGA proteins in the sunflower genome, which were unequally distributed across 17 chromosomes. Employing phylogenetic analysis encompassing 149 TGA members among 13 distinct species, we revealed the evolutionary conservation of TGA proteins across the plant kingdom. Collinearity analysis suggested that both HaTGA01 and HaTGA03 were generated due to HaTGA08 gene duplication. Notably, qRT-PCR analysis demonstrated that HaTGA04, HaTGA05, and HaTGA14 genes were remarkably upregulated under ABA, MeJA, and salt treatments, whereas HaTGA03, HaTGA06, and HaTGA07 were significantly repressed. This study contributes valuable perspectives on the potential roles of the HaTGA gene family under various stress conditions in sunflowers, thereby enhancing our understanding of TGA gene family dynamics and function within this agriculturally significant species.

Prebiotic Strategies to Manage Lactose Intolerance Symptoms.

Lactose intolerance, which affects about 65-75% of the world's population, is caused by a genetic post-weaning deficiency of lactase, the enzyme required to digest the milk sugar lactose, called lactase non-persistence. Symptoms of lactose intolerance include abdominal pain, bloating and diarrhea. Genetic variations, namely lactase persistence, allow some individuals to metabolize lactose effectively post-weaning, a trait thought to be an evolutionary adaptation to dairy consumption. Although lactase non-persistence cannot be altered by diet, prebiotic strategies, including the consumption of galactooligosaccharides (GOSs) and possibly low levels of lactose itself, may shift the microbiome and mitigate symptoms of lactose consumption. This review discusses the etiology of lactose intolerance and the efficacy of prebiotic approaches like GOSs and low-dose lactose in symptom management.

Enhancing cryo-EM structure prediction with DeepTracer and AlphaFold2 integration.

Understanding the protein structures is invaluable in various biomedical applications, such as vaccine development. Protein structure model building from experimental electron density maps is a time-consuming and labor-intensive task. To address the challenge, machine learning approaches have been proposed to automate this process. Currently, the majority of the experimental maps in the database lack atomic resolution features, making it challenging for machine learning-based methods to precisely determine protein structures from cryogenic electron microscopy density maps. On the other hand, protein structure prediction methods, such as AlphaFold2, leverage evolutionary information from protein sequences and have recently achieved groundbreaking accuracy. However, these methods often require manual refinement, which is labor intensive and time consuming. In this study, we present DeepTracer-Refine, an automated method that refines AlphaFold predicted structures by aligning them to DeepTracers modeled structure. Our method was evaluated on 39 multi-domain proteins and we improved the average residue coverage from 78.2 to 90.0% and average local Distance Difference Test score from 0.67 to 0.71. We also compared DeepTracer-Refine with Phenixs AlphaFold refinement and demonstrated that our method not only performs better when the initial AlphaFold model is less precise but also surpasses Phenix in run-time performance.

New insights into pterosaur cranial anatomy: X-ray imaging reveals palatal structure and evolutionary trends.

Among the least studied portion of the pterosaur skeleton is the palate, which tends to be poorly preserved and commonly only visible from one side (the ventral portion). Even in well-preserved specimens, the bones tend to be fused, with the limits of individual palatal elements obscured. To shed new light on this region, we employed advanced X-ray imaging techniques on the non-pterodactyloid Kunpengopterus (Wukongopteridae), and the pterodactyloids Dsungaripterus (Dsungaripteridae), Hongshanopterus (Istiodactylidae), and Hamipterus (Hamipteridae). Our analyses revealed the presence of sutures between palatal bones in Dsungaripterus and Kunpengopterus, which resulted in different interpretations of the relation between palatine, ectopterygoid, and pterygoid, leading to a new identification of the palatal openings. Furthermore, our study shows six main observations such as the variation of the angle between the palatine rami and the variation in the relative sizes of the palatal openings. We also point out that the presence of a maxillopalatine fenestra (previously identified as postpalatine fenestra), is unique within Diapsida. Although much more work needs to be done, we showed that advanced X-ray imaging techniques open a window for understanding pterosaur cranial anatomy and provide a new perspective for investigating the evolutionary history of these flying reptiles.

A region of suppressed recombination misleads neoavian phylogenomics.

Genomes are typically mosaics of regions with different evolutionary histories. When speciation events are closely spaced in time, recombination makes the regions sharing the same history small, and the evolutionary history changes rapidly as we move along the genome. When examining rapid radiations such as the early diversification of Neoaves 66 Mya, typically no consistent history is observed across segments exceeding kilobases of the genome. Here, we report an exception. We found that a 21-Mb region in avian genomes, mapped to chicken chromosome 4, shows an extremely strong and discordance-free signal for a history different from that of the inferred species tree. Such a strong discordance-free signal, indicative of suppressed recombination across many millions of base pairs, is not observed elsewhere in the genome for any deep avian relationships. Although long regions with suppressed recombination have been documented in recently diverged species, our results pertain to relationships dating circa 65 Mya. We provide evidence that this strong signal may be due to an ancient rearrangement that blocked recombination and remained polymorphic for several million years prior to fixation. We show that the presence of this region has misled previous phylogenomic efforts with lower taxon sampling, showing the interplay between taxon and locus sampling. We predict that similar ancient rearrangements may confound phylogenetic analyses in other clades, pointing to a need for new analytical models that incorporate the possibility of such events.

Style head in Apocynaceae: a very complex secretory activity performed by one tissue.

Nuptial glands are very diverse and associated with different pollination mechanisms. The greater the specificity in the pollen transfer mechanism from anther to stigma, the greater the morphological elaboration of flowers and functional complexity of the nuptial glands. In Apocynaceae, pollination mechanisms reached an extreme specificity, a fact that was only possible due to an extreme morphological synorganization and a profusion of floral glands. Although these glands are of different types, the vast majority have secretory cells only in the epidermis. In general, these epidermal cells produce many different compounds at the same time, and previous studies have demonstrated that in the style head, the functional complexity of epidermis has become even greater. Four types of style head are found in the family, which have different degrees of functional complexity in relation to the secretion produced and pollen dispersal mechanism. The secretion is fluid in types I, II and III, and the pollen is dispersed and adhered to the pollinator by the secretion produced by the style head. In type IV, the secretion hardens and acquires a specific shape, moulded by the spatial constraints of the adjacent floral organs. This evolutionary alteration is accompanied by changes in the structure and arrangement of the secretory cells, as well as in pollen aggregation and position of stigma. Histochemical analysis has shown that the secretion is mixed and highly complex, especially in the style head type IV, where the secretion, called translator, is formed by a rigid central portion, which adheres to the pollinator, and two caudicles that attach to two pollinia. The translator has a distinct composition in its different parts. Further studies are needed to answer the new questions that have arisen from the discovery of this highly functional complexity of the secretory tissue.

The ratting of North America: A 350-year retrospective on Rattus species compositions and competition.

While the impacts of black (Rattus rattus) and brown (Rattus norvegicus) rats on human society are well documented-including the spread of disease, broad-scale environmental destruction, and billions spent annually on animal control-little is known about their ecology and behavior in urban areas due to the challenges of studying animals in city environments. We use isotopic and ZooMS analysis of archaeological (1550s-1900 CE) rat remains from eastern North America to provide a large-scale framework for species arrival, interspecific competition, and dietary ecology. Brown rats arrived earlier than expected and rapidly outcompeted black rats in coastal urban areas. This replacement happened despite evidence that the two species occupy different trophic positions. Findings include the earliest molecularly confirmed brown rat in the Americas and show a deep ecological structure to how rats exploit human-structured areas, with implications for understanding urban zoonosis, rat management, and ecosystem planning as well as broader themes of rat dispersal, phylogeny, evolutionary ecology, and climate impacts.

Coadaptation of coexisting plants enhances productivity in an agricultural system.

Growing crops in more diverse crop systems (i.e., intercropping) is one way to produce food more sustainably. Even though intercropping, compared to average monocultures, is generally more productive, the full yield potential of intercropping might not yet have been achieved as modern crop cultivars are bred to be grown in monoculture. Breeding plants for more familiarity in mixtures, i.e., plants that are adapted to more diverse communities (i.e., adaptation) or even to coexist with each other (i.e., coadaptation) might have the potential to sustainably enhance productivity. In this study, the productivity benefits of familiarity through evolutionary adaptation and coevolutionary coadaptation were disentangled in a crop system through an extensive common garden experiment. Furthermore, evolutionary and coevolutionary effects on species-level and community-level productivity were linked to corresponding changes in functional traits. We found evidence for higher productivity and trait convergence with increasing familiarity with the plant communities. Furthermore, our results provide evidence for the coevolution of plants in mixtures leading to higher productivity of coadapted species. However, with the functional traits measured in our study, we could not fully explain the productivity benefits found upon coevolution. Our study investigated coevolution among randomly interacting plants and was able to demonstrate that coadaptation through coevolution of coexisting species in mixtures occurs and promotes ecosystem functioning (i.e., higher productivity). This result is particularly relevant for the diversification of agricultural and forest ecosystems, demonstrating the added value of artificially selecting plants for the communities they are familiar with.

[Comparative analysis of plastomes of Rubus chingii and R. chingii var. suavissimus].

Rubus chingii and R. chingii var. suavissimus are unique dual-purpose plant resources, with significant nutraceutical, pharmaceutical, and economic value, as well as promising prospects for further development. To investigate the genetic structure and evolutionary characteristics of these two varieties, this study conducted plastome sequencing using the Illumina HiSeq XTen sequencing platform. Subsequently, the study performed assembly, annotation, and characterization of the genomes, followed by a comparative plastome and phylogenetic analysis using bioinformatics techniques. The results revealed that the plastomes of R. chingii and R. chingii var. suavissimus exhibited a tetrad structure, comprising a large single-copy region(LSC), a small single-copy region(SSC), and two inverted repeat regions(IRs). The study identified a total of 56 simple sequence repeats(SSRs) after comparative analysis, predominantly consisting of A and T. Furthermore, the structure of the IR boundary genes in both varieties was found to be highly conserved, with only minor nucleotide variations. Additionally, the study identified three highly variable regions: rps16-trnQ-psbK, trnR-atpA, and trnT-trnL, which held promise as potential identification marks for further development and utilization. Phylogenetic analysis results obtained by the maximum likelihood and Bayesian inference methods demonstrated a close clustering of R. chingii and R. chingii var. suavissimus(100% support), with their closest relatives being R. trianthus. This study, focusing on plastome-level genetic distinctions between these two varieties, lays a foundation for future species protection, development, and utilization.

Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks.

The emergence of viral variants with altered phenotypes is a public health challenge underscoring the need for advanced evolutionary forecasting methods. Given extensive epistatic interactions within viral genomes and known viral evolutionary history, efficient genomic surveillance necessitates early detection of emerging viral haplotypes rather than commonly targeted single mutations. Haplotype inference, however, is a significantly more challenging problem precluding the use of traditional approaches. Here, using SARS-CoV-2 evolutionary dynamics as a case study, we show that emerging haplotypes with altered transmissibility can be linked to dense communities in coordinated substitution networks, which become discernible significantly earlier than the haplotypes become prevalent. From these insights, we develop a computational framework for inference of viral variants and validate it by successful early detection of known SARS-CoV-2 strains. Our methodology offers greater scalability than phylogenetic lineage tracing and can be applied to any rapidly evolving pathogen with adequate genomic surveillance data.

Osteohistological insight into the growth dynamics of early dinosaurs and their contemporaries.

Dinosauria debuted on Earth's stage in the aftermath of the Permo-Triassic Mass Extinction Event, and survived two other Triassic extinction intervals to eventually dominate terrestrial ecosystems. More than 231 million years ago, in the Upper Triassic Ischigualasto Formation of west-central Argentina, dinosaurs were just getting warmed up. At this time, dinosaurs represented a minor fraction of ecosystem diversity. Members of other tetrapod clades, including synapsids and pseudosuchians, shared convergently evolved features related to locomotion, feeding, respiration, and metabolism and could have risen to later dominance. However, it was Dinosauria that radiated in the later Mesozoic most significantly in terms of body size, diversity, and global distribution. Elevated growth rates are one of the adaptations that set later Mesozoic dinosaurs apart, particularly from their contemporary crocodilian and mammalian compatriots. When did the elevated growth rates of dinosaurs first evolve? How did the growth strategies of the earliest known dinosaurs compare with those of other tetrapods in their ecosystems? We studied femoral bone histology of an array of early dinosaurs alongside that of non-dinosaurian contemporaries from the Ischigualasto Formation in order to test whether the oldest known dinosaurs exhibited novel growth strategies. Our results indicate that the Ischigualasto vertebrate fauna collectively exhibits relatively high growth rates. Dinosaurs are among the fastest growing taxa in the sample, but they occupied this niche alongside crocodylomorphs, archosauriformes, and large-bodied pseudosuchians. Interestingly, these dinosaurs grew at least as quickly, but more continuously than sauropodomorph and theropod dinosaurs of the later Mesozoic. These data suggest that, while elevated growth rates were ancestral for Dinosauria and likely played a significant role in dinosaurs' ascent within Mesozoic ecosystems, they did not set them apart from their contemporaries.

Replicator-mutator dynamics with evolutionary public goods game-environmental feedbacks.

Feedback loops between strategies and the environment are commonly observed in socio-ecological, evolution-ecological, and psychology-economic systems. However, the impact of mutations in these feedback processes is often overlooked. This study proposes a novel model that integrates the public goods game with environmental feedback, considering the presence of mutations. In our model, the enhancement factor of the public goods game combines positive and negative incentives from the environment. By employing replicator-mutator (RM) equations, we provide an objective understanding of the system's evolutionary state, focusing on identifying conditions that foster cooperation and prevent the tragedy of the commons. Specifically, mutations play a crucial role in the RM dynamics, leading to the emergence of an oscillatory tragedy of the commons. By verifying the Hopf bifurcation condition, we establish the existence of a stable limit cycle, providing valuable insights into sustained oscillation strategies. Moreover, the feedback mechanism inherent in the public goods game model offers a fresh perspective on effectively addressing the classic dilemma of the tragedy of the commons.

Reproductive system, temperature, and genetic background effects in experimentally evolving populations of Caenorhabditis elegans.

Experimental evolution (EE) is a powerful research framework for gaining insights into many biological questions, including the evolution of reproductive systems. We designed a long-term and highly replicated EE project using the nematode C. elegans, with the main aim of investigating the impact of reproductive system on adaptation and diversification under environmental challenge. From the laboratory-adapted strain N2, we derived isogenic lines and introgressed the fog-2(q71) mutation, which changes the reproductive system from nearly exclusive selfing to obligatory outcrossing, independently into 3 of them. This way, we obtained 3 pairs of isogenic ancestral populations differing in reproductive system; from these, we derived replicate EE populations and let them evolve in either novel (increased temperature) or control conditions for over 100 generations. Subsequently, fitness of both EE and ancestral populations was assayed under the increased temperature conditions. Importantly, each population was assayed in 2-4 independent blocks, allowing us to gain insight into the reproducibility of fitness scores. We expected to find upward fitness divergence, compared to ancestors, in populations which had evolved in this treatment, particularly in the outcrossing ones due to the benefits of genetic shuffling. However, our data did not support these predictions. The first major finding was very strong effect of replicate block on populations' fitness scores. This indicates that despite standardization procedures, some important environmental effects were varying among blocks, and possibly compounded by epigenetic inheritance. Our second key finding was that patterns of EE populations' divergence from ancestors differed among the ancestral isolines, suggesting that research conclusions derived for any particular genetic background should never be generalized without sampling a wider set of backgrounds. Overall, our results support the calls to pay more attention to biological variability when designing studies and interpreting their results, and to avoid over-generalizations of outcomes obtained for specific genetic and/or environmental conditions.