A Dysfunctional Sense of Smell: The Irreversibility of Olfactory Evolution in Free-Living Pigs

The natural diet composition of young piglets suggests an overlook of fibre and food structure in farmed suckling piglets

BACKGROUND

The often disappointing intake of creep feed by suckling piglets coincides with a limited ability to cope with challenges such as weaning diarrhoea. Investigating the dietary nutrient profile of piglets (Sus scrofa) in the wild may help to improve nutrition for farmed piglets. This study was conducted to analyse the stomach content of feral piglets and their farmed counterparts, and to compare them with the composition of commercial creep feeds. Forty feral piglets (4.6 ± 1.4 kg) living in a wild herd were tracked and legally hunted in the Bahía Samborombón (Buenos Aires, Argentina). Their gastric contents were collected for analysing macronutrients. Twenty-eight farmed suckling piglets of similar ages were sourced from a Dutch research farm, and their stomach contents were collected and pooled into fourteen samples with the same procedure for comparison. Additionally, the composition data of twenty-five commercial feeds was also collected.

RESULTS

A higher dry matter content was observed in the farmed piglets' stomachs (233 vs. 148 g/kg, P < 0.05). The gastric crude protein concentration was similar between both groups but the crude fat concentration was higher in the stomach of farmed animals (525 vs. 238 g/kg DM, P < 0.05), while feral piglets consumed more ash and fibre (P < 0.05). A similar concentration of non-fibrous carbohydrates (NFC) on metabolizable energy basis was observed by calculation through the NRC's guideline (P > 0.05). Within the fibre content, significantly greater concentrations of neutral detergent fiber (NDF), acid detergent fiber (ADF) and acid detergent lignin (ADL) were observed in the stomach of feral piglets than in those of farmed piglets (282 vs. 36 g/kg, 158 vs. 9 g/kg DM, 53 vs. 3 g/kg DM, respectively, P < 0.05). Similar protein concentrations were observed between the gastric content of feral piglets and creep feed, while significantly higher crude ash and crude fat concentrations were found in feral piglets' consumption (P < 0.05).

CONCLUSION

In conclusion, piglets in natural conditions consume much more fibre-from coarse plant material-compared to farmed piglets receiving creep feed. Although technical performance is distinctly different between nature and farm, it raises the question whether suckling piglets under farming conditions would benefit from a more fibrous and coarser creep feed.

The effects of runs-of-homozygosity on pig domestication and breeding

BACKGROUND

Since their domestication, recent inbreeding together with intensive artificial selection and population bottlenecks have allowed the prevalence of deleterious mutations and the increase of runs-of-homozygosity (ROH) in domestic pigs. This makes pigs a good model to understand the genetic underpinnings of inbreeding depression.

RESULTS

Here we integrated a comprehensive dataset comprising 7239 domesticated pigs and wild boars genotyped by single nucleotide polymorphism (SNP) chips, along with phenotypic data encompassing growth, reproduction and disease-associated traits. Our study revealed differential ROH landscapes during domestication and artificial selection of Eurasian pigs. We observed associations between ROH burden and phenotypic traits such as body conformation and susceptibility to diseases like scrotal hernia. By examining associations of whole-genome and regional ROH burden with gene expression, we identified specific genes and pathways affected by inbreeding depression. Associations of regional ROH burden with gene expression also enabled the discovery of novel regulatory elements. Lastly, we inferred recessive lethal mutations by examining depletion of ROH in an inbred population with relatively small sample size, following by fine mapping with sequencing data.

CONCLUSIONS

These findings suggested that both phenotypic and genetic variations have been reshaped by inbreeding, and provided insights to the genetic mechanisms underlying inbreeding depression.

Navigating discreetly: Spatial ecology of urban wild boar in Bordeaux City's landscape of fear, France

An exemplary urban adapter, the wild boar (Sus scrofa) has successfully colonized urban ecological niches worldwide. Improvement of strategies for optimal management of urban wild boar need to gather more empirical evidence of their spatial ecology. This study is based on GPS tracking and capture-mark-recapture (CMR) of 10 and 59 wild boar, respectively, captured in Bordeaux Metropolis (France). It shows that wild boar have become urban dwellers, with intra-urban home ranges varying from 1.3 to 64.6 km2 (MCP 100 %) and from 0.5 to 9.6 km2 (KDE 95 %), depending on urban conditions. CMR results confirm the low propensity to move away from urban areas (with a mean distance of 2 km between capture and recapture sites), despite a relatively low one-year survival rate since capture (47.5 %), primarily attributable to removal efforts. Wild boar strongly depended on urban woods, mostly during daytime resting, and highly frequented urban meadows during night foraging. Their use of urban agricultural areas was minimal, but they were mostly monitored following corn and grape harvests. Wild boar mitigated the risk associated with close proximity to humans by: a nocturnal activity (72.2 % of active locations registered from sunset to sunrise), which could also be partially attributed to their sensitivity to heat; a strong use of covered habitats, especially during daytime resting and when close to buildings and roads; and a low mobility during night-time foraging (1974 m average daily distance travelled). Moreover, we demonstrate high inter- and intra-individual variability in the spatio-temporal behaviour of urban wild boar. Finally, we discuss the gap between these results and the narratives surrounding the spatial ecology of urban wild boar. Our results not only confirm the species' ability to adapt to urban environments, but also highlight their behavioural flexibility, underscoring the relevance of significant changes in representations and management activities to mitigate human-urban wild boar conflicts.

How domestication, feralization and experience-dependent plasticity affect brain size variation in Sus scrofa

Among domestic species, pigs experienced the greatest brain size reduction, but the extent and factors of this reduction remain unclear. Here, we used the brain endocast volume collected from 92 adult skulls of wild, captive, feral and domestic Sus scrofa to explore the effects of domestication, feralization and captivity over the brain size variation of this species. We found a constant brain volume increase over 24 months, while body growth slowed down from month 20. We observed an 18% brain size reduction between wild boars and pigs, disagreeing with the 30%-40% reduction previously mentioned. We did not find significant sexual differences in brain volume, refuting the theory of the attenuation of male secondary sexual characteristics through the selection for reduced male aggression. Feralization in Australia led to brain size reduction-probably as an adaptation to food scarcity and drought, refuting the reversal to wild ancestral brain size. Finally, free-born wild boars raised in captivity showed a slight increase in brain size, potentially due to a constant and high-quality food supply as well as new allospecific interactions. These results support the need to further explore the influence of diet, environment and experience on brain size evolution during animal domestication.

The Domestication of Wild Boar Could Result in a Relaxed Selection for Maintaining Olfactory Capacity

Domesticated animals are artificially selected to exhibit desirable traits, however not all traits of domesticated animals are the result of deliberate selection. Loss of olfactory capacity in the domesticated pig (Sus scrofa domesticus) is one example. We used whole transcriptome analysis (RNA-Seq) to compare patterns of gene expression in the olfactory mucosa of the pig and two subspecies of wild boar (Sus scrofa), and investigate candidate genes that could be responsible for the loss of olfactory capacity. We identified hundreds of genes with reductions in transcript abundance in pig relative to wild boar as well as differences between the two subspecies of wild boar. These differences were detected mainly in genes involved in the formation and motility of villi, cilia and microtubules, functions associated with olfaction. In addition, differences were found in the abundances of transcripts of genes related to immune defenses, with the highest levels in continental wild boar subspecies. Overall, the loss of olfactory capacity in pigs appears to have been accompanied by reductions in the expression of candidate genes for olfaction. These changes could have resulted from unintentional selection for reduced olfactory capacity, relaxed selection for maintaining olfactory capacity, pleiotropic effects of genes under selection, or other non-selective processes. Our findings could be a cornerstone for future researches on wild boars, pigs, feral populations, and their evolutionary trajectories, aimed to provide tools to better calibrate species management as well as guidelines for breeders.

Domestication effect of reduced brain size is reverted when mink become feral

A typical consequence of breeding animal species for domestication is a reduction in relative brain size. When domesticated animals escape from captivity and establish feral populations, the larger brain of the wild phenotype is usually not regained. In the American mink (Neovison vison), we found an exception to this rule. We confirmed the previously described reduction in relative braincase size and volume compared to their wild North American ancestors in mink bred for their fur in Poland, in a dataset of 292 skulls. We then also found a significant regrowth of these measures in well-established feral populations in Poland. Closely related, small mustelids are known for seasonal reversible changes in skull and brain size. It seems that these small mustelids are able to regain the brain size, which is adaptive for living in the wild, and flexibly respond to selection accordingly.

Reprogramming of the gut microbiota following feralization in Sus scrofa

BACKGROUND

Wild boar has experienced several evolutionary trajectories from which domestic (under artificial selection) and the feral pig (under natural selection) originated. Strong adaptation deeply affects feral population's morphology and physiology, including the microbiota community. The gut microbiota is generally recognized to play a crucial role in maintaining host health and metabolism. To date, it is unclear whether feral populations' phylogeny, development stages or lifestyle have the greatest impact in shaping the gut microbiota, as well as how this can confer adaptability to new environments. Here, in order to deepen this point, we characterized the gut microbiota of feral population discriminating between juvenile and adult samples, and we compared it to the microbiota structure of wild boar and domestic pig as the references. Gut microbiota composition was estimated through the sequencing of the partial 16S rRNA gene by DNA metabarcoding and High Throughput Sequencing on DNA extracted from fecal samples.

RESULTS

The comparison of microbiota communities among the three forms showed significant differences. The feral form seems to carry some bacteria of both domestic pigs, derived from its ancestral condition, and wild boars, probably as a sign of a recent re-adaptation strategy to the natural environment. In addition, interestingly, feral pigs show some exclusive bacterial taxa, also suggesting an innovative nature of the evolutionary trajectories and an ecological segregation in feral populations, as already observed for other traits.

CONCLUSIONS

The feral pig showed a significant change between juvenile and adult microbiota suggesting an influence of the wild environment in which these populations segregate. However, it is important to underline that we certainly cannot overlook that these variations in the structure of the microbiota also depended on the different development stages of the animal, which in fact influence the composition of the intestinal microbiota. Concluding, the feral pigs represent a new actor living in the same geographical space as the wild boars, in which its gut microbial structure suggests that it is mainly the result of environmental segregation, most different from its closest relative. This gives rise to interesting fields of exploration regarding the changed ecological complexity and the consequent evolutionary destiny of the animal communities involved in this phenomenon.

Local-scale habitat configuration makes a niche for wildlife encroaching into an urban landscape: grubbing sites of wild boar Sus scrofa in a city matrix

Urban environments may offer certain species diverse and abundant food resources of natural and anthropogenic origin. However, the local-scale configuration of habitats and urban infrastructure may influence foraging decisions regardless of the availability of food. In recent years, the expansion of wild boar Sus scrofa into areas significantly transformed by humans has been observed in many parts of its range. Grubbing (rooting) is a major foraging mode of the species, during which disturbance of the upper soil layers enables these animals to find and consume food items. However, the factors that determine the selection of grubbing sites in the urban landscape, where the balance between food availability and the avoidance of humans may influence foraging decisions, are not known. Our aim was to identify local-scale factors that influence grubbing site selection and the size of grubbed patches in an urban landscape. The characteristics of 108 wild boar grubbing sites in the city of Kraków (Poland) were compared to randomly selected control sites. The probable presence of a grubbing site was positively correlated with the proportion of meadows and fallow land in the vicinity and with increases in both canopy cover and distance to pavements. The size of a grubbed patch was positively correlated with the percentage of meadows in the vicinity, increasing distance to buildings and decreasing distance to pavements. We found a non-random pattern of grubbing sites in the urban landscape and indicated that the local-scale configuration of vegetation and urban infrastructure contribute to foraging site selection by wild boar. Our study highlights that the encroachment of wildlife into the urban landscape is a complex process, driven by both resource availability and the avoidance of human-related disturbances.

The Boar War: Five Hot Factors Unleashing Boar Expansion and Related Emergency

The recent and ever-growing problem of boar (Sus scrofa forms including wild boar, hybrid and feral pig) expansion is a very complex issue in wildlife management. The damages caused to biodiversity and the economies are addressed in different ways by the various countries, but research is needed to shed light on the causal factors of this emergency before defining a useful collaborative management policy. In this review, we screened more than 280 references published between 1975–2022, identifying and dealing with five hot factors (climate change, human induced habitat modifications, predator regulation on the prey, hybridization with domestic forms, and transfaunation) that could account for the boar expansion and its niche invasion. We also discuss some issues arising from this boar emergency, such as epizootic and zoonotic diseases or the depression of biodiversity. Finally, we provide new insights for the research and the development of management policies.

Population genomic, olfactory, dietary, and gut microbiota analyses demonstrate the unique evolutionary trajectory of feral pigs

Domestication is an intriguing evolutionary process. Many domestic populations are subjected to strong human-mediated selection, and when some individuals return to the wild, they are again subjected to selective forces associated with new environments. Generally, these feral populations evolve into something different from their wild predecessors and their members typically possess a combination of both wild and human selected traits. Feralisation can manifest in different forms on a spectrum from a wild to a domestic phenotype. This depends on how the rewilded domesticated populations can readapt to natural environments based on how much potential and flexibility the ancestral genome retains after its domestication signature. Whether feralisation leads to the evolution of new traits that do not exist in the wild or to convergence with wild forms, however, remains unclear. To address this question, we performed population genomic, olfactory, dietary, and gut microbiota analyses on different populations of Sus scrofa (wild boar, hybrid, feral and several domestic pig breeds). Porcine single nucleotide polymorphisms (SNPs) analysis shows that the feral population represents a cluster distinctly separate from all others. Its members display signatures of past artificial selection, as demonstrated by values of FST in specific regions of the genome and bottleneck signature, such as the number and length of runs of homozygosity. Generalised FST values, reacquired olfactory abilities, diet, and gut microbiota variation show current responses to natural selection. Our results suggest that feral pigs are an independent evolutionary unit which can persist so long as levels of human intervention remain unchanged.

Genome-wide scan for runs of homozygosity identifies candidate genes in Wannan Black pigs

Objective

Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that can reveal inbreeding levels, selection pressure, and mating schemes. In this study, ROHs were evaluated in Wannan Black pigs to assess the inbreeding levels and the genome regions with high ROH frequency.

Methods

In a previous study, we obtained 501.52 GB of raw data from resequencing (10×) of the genome and identified 21,316,754 single-nucleotide variants in 20 Wannan Black pig samples. We investigated the number, length, and frequency of ROH using resequencing data to characterize the homozygosity in Wannan Black pigs and identified genomic regions with high ROH frequencies.

Results

In this work, 1,813 ROHs (837 ROHs in 100 to 500 kb, 449 ROHs in 500 to 1,000 kb, 527 ROHs in >1,000 kb) were identified in all samples, and the average genomic inbreeding coefficient (F_ROH) in Wannan Black pigs was 0.5234. Sixty-one regions on chromosomes 2, 3, 7, 8, 13, 15, and 16 harbored ROH islands. In total, 105 genes were identified in 42 ROH islands, among which some genes were related to production traits.

Conclusion

This is the first study to identify ROH across the genome of Wannan Black pigs, the Chinese native breed of the Anhui province. Overall, Wannan Black pigs have high levels of inbreeding due to the influence of ancient and recent inbreeding due to the genome. These findings are a reliable resource for future studies and contribute to save and use the germplasm resources of Wannan Black pigs.

Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals

Background

In response to ecological niche of domestication, domesticated mammals and birds developed adaptively phenotypic homoplasy in behavior modifications like fearlessness, altered sociability, exploration and cognition, which partly or indirectly result in consequences for economic productivity. Such independent adaptations provide an excellent model to investigate molecular mechanisms and patterns of evolutionary convergence driven by artificial selection.

Results

First performing population genomic and brain transcriptional comparisons in 68 wild and domesticated chickens, we revealed evolutionary trajectories, genetic architectures and physiologic bases of adaptively behavioral alterations. To extensively decipher molecular convergence on behavioral changes thanks to domestication, we investigated selection signatures in hundreds of genomes and brain transcriptomes across chicken and 6 other domesticated mammals. Although no shared substitution was detected, a common enrichment of the adaptive mutations in regulatory sequences was observed, presenting significance to drive adaptations. Strong convergent pattern emerged at levels of gene, gene family, pathway and network. Genes implicated in neurotransmission, semaphorin, tectonic protein and modules regulating neuroplasticity were central focus of selection, supporting molecular repeatability of homoplastic behavior reshapes. Genes at nodal positions in trans-regulatory networks were preferably targeted. Consistent down-regulation of majority brain genes may be correlated with reduced brain size during domestication. Up-regulation of splicesome genes in chicken rather mammals highlights splicing as an efficient way to evolve since avian-specific genomic contraction of introns and intergenics. Genetic burden of domestication elicits a general hallmark. The commonly selected genes were relatively evolutionary conserved and associated with analogous neuropsychiatric disorders in human, revealing trade-off between adaption to life with human at the cost of neural changes affecting fitness in wild.

Conclusions

After a comprehensive investigation on genomic diversity and evolutionary trajectories in chickens, we revealed basis, pattern and evolutionary significance of molecular convergence in domesticated bird and mammals, highlighted the genetic basis of a compromise on utmost adaptation to the lives with human at the cost of high risk of neurophysiological changes affecting animals’ fitness in wild.

Pre-birth sense of smell in the wild boar: the ontogeny of the olfactory mucosa

Animals recognize their surrounding environments through the sense of smell by detecting thousands of chemical odorants. Wild boars (Sus scrofa) completely depend on their ability to recognize chemical odorants: to detect food, during scavenging and searching partners, during breeding periods and to avoid potential predators. Wild piglets must be prepared for the chemical universe that they will enter after birth, and they show intense neuronal activity in the olfactory mucosa. With this in mind, we investigated the morpho-functional embryonic development of the olfactory mucosa in the wild boar (in five stages before birth). Using mRNA expression analysis of olfactory marker protein and neuropeptide Y, involved in the function of olfactory sensory neurons, we show early activation of the appropriate genes in the wild boar. We hypothesize olfactory pre-birth development in wild boar is highly adaptive.

Unexpected but welcome. Artificially selected traits may increase fitness in wild boar

Artificial selection affects phenotypes differently by natural selection. Domestic traits, which pass into the wild, are usually negatively selected. Yet, exceptionally, this axiom may fail to apply if genes, from the domestic animals, increase fertility in the wild. We studied a rare case of a wild boar population under the framework of Wright's interdemic selection model, which could explain gene flow between wild boar and pig, both considered as demes. We analysed the MC1R gene and microsatellite neutral loci in 62 pregnant wild boars as markers of hybridization, and we correlated nucleotide mutations on MC1R (which are common in domestic breeds) to litter size, as an evaluation of fitness in wild sow. Regardless of body size and phyletic effects, wild boar sows bearing nonsynonymous MC1R mutations produced larger litters. This directly suggests that artificially selected traits reaching wild populations, through interdemic gene flow, could bypass natural selection if and only if they increase the fitness in the wild.

Modeling and mapping the probability of occurrence of invasive wild pigs across the contiguous United States

Wild pigs (Sus scrofa), also known as wild swine, feral pigs, or feral hogs, are one of the most widespread and successful invasive species around the world. Wild pigs have been linked to extensive and costly agricultural damage and present a serious threat to plant and animal communities due to their rooting behavior and omnivorous diet. We modeled the current distribution of wild pigs in the United States to better understand the physiological and ecological factors that may determine their invasive potential and to guide future study and eradication efforts. Using national-scale wild pig occurrence data reported between 1982 and 2012 by wildlife management professionals, we estimated the probability of wild pig occurrence across the United States using a logistic discrimination function and environmental covariates hypothesized to influence the distribution of the species. Our results suggest the distribution of wild pigs in the U.S. was most strongly limited by cold temperatures and availability of water, and that they were most likely to occur where potential home ranges had higher habitat heterogeneity, providing access to multiple key resources including water, forage, and cover. High probability of occurrence was also associated with frequent high temperatures, up to a high threshold. However, this pattern is driven by pigs’ historic distribution in warm climates of the southern U.S. Further study of pigs’ ability to persist in cold northern climates is needed to better understand whether low temperatures actually limit their distribution. Our model highlights areas at risk of invasion as those with habitat conditions similar to those found in pigs’ current range that are also near current populations. This study provides a macro-scale approach to generalist species distribution modeling that is applicable to other generalist and invasive species.

Immunocytochemical characterisation of ensheathing glia in the olfactory and vomeronasal systems of Ambystoma mexicanum (Caudata: Ambystomatidae)

The olfactory and vomeronasal systems of vertebrates are characterised by neurogenesis occurring throughout life. The regenerative ability of olfactory receptor neurons relies on specific glial cells, the olfactory and vomeronasal axon-surrounding cells. Numerous studies have examined mammalian olfactory ensheathing cells which are considered potential candidates for spinal cord injury repair using cell-based therapy. With regard to non-mammalian vertebrates, limited information is available on these glial cells in fish, and there is no information on them in terrestrial anamniotes, the amphibians. In the present research, we studied the immunocytochemical characteristics of axon-surrounding cells in Ambystoma mexicanum. Urodeles have relatively simple olfactory and vomeronasal systems, and represent a good model for studying ensheathing cells in extant representatives of basal tetrapods. Sections from the decalcified heads of A. mexicanum were immunocytochemically processed for the detection of proteins used in research on mammalian olfactory-ensheathing cells. S100, GFAP and NCAM were clearly observed. p75NTR, Gal-1 and PSA-NCAM showed weak staining. No vimentin immunopositivity was observed. The corresponding areas of the olfactory and vomeronasal pathways displayed the same staining characteristics, with the exception of Gal-1, p75NTR and PSA-NCAM in the mucosae. The degree of marker expression was not uniform throughout the sensory pathways. In contrast to fish, both olfactory and vomeronasal nerves displayed uniform staining intensity. This study showed that some markers for mammalian and fish-ensheathing glia are also applicable in urodeles. The olfactory systems of vertebrates show similarities, and also clear dissimilarities. Further investigations are required to ascertain the functional significance of these regional and interspecific differences.