Selection for reluctance to avoid humans during the domestication of mice

Comparison of the exploratory behaviour of wild and laboratory mouse species

In this study, we compared the exploratory behaviour of mound-building mice (Mus spicilegus) and house mice (Mus musculus) with domesticated laboratory mouse strains (BALB/c and C57BL/6). The animals spent 15 minutes in the furnished test box before the exit to the outside world became free. During the 5-minute test, it was noted whether the animal left the familiar environment; if it did, it was recorded in how many seconds. Based on our results, the wild mouse species were more likely to leave the familiar mouse box and explore the outside environment earlier than the laboratory mice. We also found a difference within the wild mouse species, the mound-building mouse being the one that explored the external environment to a greater extent and faster. The effect of domestication manifests in the fact that laboratory mouse strains are less likely to leave their familiar environment and are significantly less active than their wild ancestors.

Association of tameness and sociability but no sign of domestication syndrome in mice selectively bred for active tameness

Domesticated animals have been developed by selecting desirable traits following the initial unconscious selection stage, and now exhibit phenotypes desired by humans. Tameness is a common behavioural trait found in all domesticated animals. At the same time, these domesticated animals exhibit a variety of morphological, behavioural, and physiological traits that differ from their wild counterparts of their ancestral species. These traits are collectively referred to as domestication syndrome. However, whether this phenomenon exists is debatable. Previously, selective breeding has been used to enhance active tameness, a motivation to interact with humans, in wild heterogeneous stock mice derived from eight wild inbred strains. In the current study, we used tame mice to study how selective breeding for active tameness affects behavioural and morphological traits. A series of behavioural and morphological analyses on mice showed an increased preference for social stimuli and a longer duration of engagement in non-aggressive behaviour. However, no differences were observed in exploratory or anxiety-related behaviours. Similarly, selection for tameness did not affect ultrasonic vocalisations in mice, and no changes were observed in known morphological traits associated with domestication syndrome. These results suggest that there may be a link between active tameness and sociability and provide insights into the relationship between tameness and other behaviours in the context of domestication.

A missense mutation in RRM1 contributes to animal tameness

The increased tameness to reduce avoidance of human in wild animals has been long proposed as the key step of animal domestication. The tameness is a complex behavior trait and largely determined by genetic factors. However, the underlying genetic mutations remain vague and how they influence the animal behaviors is yet to be explored. Behavior tests of a wild-domestic hybrid goat population indicate the locus under strongest artificial selection during domestication may exert a huge effect on the flight distance. Within this locus, only one missense mutation RRM1I241V which was present in the early domestic goat ~6500 years ago. Genome editing of RRM1I241V in mice showed increased tameness and sociability and reduced anxiety. These behavioral changes induced by RRM1I241V were modulated by the alternation of activity of glutamatergic synapse and some other synapse-related pathways. This study established a link between RRM1I241V and tameness, demonstrating that the complex behavioral change can be achieved by mutations under strong selection during animal domestication.

Genetic dissection of behavioral traits related to successful training of drug detection dogs

Drug detection dogs play integral roles in society. However, the interplay between their behaviors and genetic characteristics underlying their performance remains uninvestigated. Herein, more than 120,000 genetic variants were evaluated in 326 German Shepherd or Labrador Retriever dogs to profile the genetic traits associated with various behavioral traits related to the successful training of drug detection dogs. Behavioral breed differences were observed in 'friendliness to humans' and 'tolerance to dogs.' A genome-wide association study within both breeds identified 11 regions potentially associated with drug detection dog characteristics as well as 'interest in the target' and 'friendliness to humans,' which are related to drug detection abilities. Among them, 63 protein-coding genes, including Atat1 and Pfn2 known to be associated with anxiety-related or exploration behavior in mice, respectively, were located surrounding the identified candidate polymorphisms. This study highlights genetic characteristics associated with behavioral traits that are important for the successful training of drug detection dogs. Thus, these findings may facilitate improved breeding and training of these dogs.

Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice

Background

The laboratory mouse was domesticated from the wild house mouse. Understanding the genetics underlying domestication in laboratory mice, especially in the widely used classical inbred mice, is vital for studies using mouse models. However, the genetic mechanism of laboratory mouse domestication remains unknown due to lack of adequate genomic sequences of wild mice.

Results

We analyze the genetic relationships by whole-genome resequencing of 36 wild mice and 36 inbred strains. All classical inbred mice cluster together distinctly from wild and wild-derived inbred mice. Using nucleotide diversity analysis, Fst, and XP-CLR, we identify 339 positively selected genes that are closely associated with nervous system function. Approximately one third of these positively selected genes are highly expressed in brain tissues, and genetic mouse models of 125 genes in the positively selected genes exhibit abnormal behavioral or nervous system phenotypes. These positively selected genes show a higher ratio of differential expression between wild and classical inbred mice compared with all genes, especially in the hippocampus and frontal lobe. Using a mutant mouse model, we find that the SNP rs27900929 (T>C) in gene Astn2 significantly reduces the tameness of mice and modifies the ratio of the two Astn2 (a/b) isoforms.

Conclusion

Our study indicates that classical inbred mice experienced high selection pressure during domestication under laboratory conditions. The analysis shows the positively selected genes are closely associated with behavior and the nervous system in mice. Tameness may be related to the Astn2 mutation and regulated by the ratio of the two Astn2 (a/b) isoforms.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-022-02772-1.

Efficient genome editing in wild strains of mice using the i-GONAD method

Wild mouse strains have been used for many research studies, because of the high level of inter-strain genetic and phenotypic variations in them, in addition to the characteristic phenotype maintained from wild mice. However, since application of the current genetic engineering method on wild strains is not easy, there are limited studies that have attempted to apply gene modification techniques in wild strains. Recently, i-GONAD, a new method for genome editing that does not involve any ex vivo manipulation of unfertilized or fertilized eggs has been reported. We applied i-GONAD method for genome editing on a series of wild strains and showed that genome editing is efficiently possible using this method. We successfully made genetically engineered mice in seven out of the nine wild strains. Moreover, we believe that it is still possible to apply milder conditions and improve the efficiencies for the remaining two strains. These results will open avenues for studying the genetic basis of various phenotypes that are characteristic to wild strains. Furthermore, applying i-GONAD will be also useful for other mouse resources in which genetic manipulation is difficult using the method of microinjection into fertilized eggs.

Searching where the treasure is: on the emergence of human companion animal partnership (HCAP)

In our view, the discipline, often referred to as human-animal interaction (HAI), lacks a well-defined conceptual framework. It is too narrow both with respect to the animal species investigated and the nature of human-animal interactions studied. So instead, we introduce the term human-companion animal partnership (HCAP) that is not only a better descriptor for most research efforts within HAI but also helps to direct research efforts on an ethological basis. In our approach, 'companion' is a function and not a feature of some species. This means that many species had and could have a potential to form mixed social groups with humans if they evolve some capacity of social competence. This view may initiate new comparative research involving a range of species to find out how complex social engagement could be maintained in such hetero-specific social groups based on evolutionary heritage, recent selection and individual experience (socialisation). Our approach emphasises the role of human caring behaviour and social competence in the emergence of a partnership with several species, and thus could also help in setting expectations for welfare and aid in designing artificial companions for specific purposes.

Combined change of behavioral traits for domestication and gene-networks in mice selectively bred for active tameness

Tameness is a major element of animal domestication and involves two components: motivation to approach humans (active tameness) and reluctance to avoid humans (passive tameness). To understand the behavioral and genetic mechanisms of active tameness in mice, we had previously conducted selective breeding for long durations of contact and heading toward human hands in an active tameness test using a wild-derived heterogeneous stock. Although the study showed a significant increase in contacting and heading with the 12th generation of breeding, the effect on other behavioral indices related to tameness and change of gene expression levels underlying selective breeding was unclear. Here, we analyzed nine tameness-related traits at a later stage of selective breeding and analyzed how gene expression levels were changed by the selective breeding. We found that five traits, including contacting and heading, showed behavioral change in the selective groups comparing to the control through the generations. Furthermore, we conducted cluster analyses to evaluate the relationships among the nine traits and found that contacting and heading combined in an independent cluster in the selected groups, but not in the control groups. RNA-Seq of hippocampal tissue revealed differential expression of 136 genes between the selection and control groups, while the pathway analysis identified the networks associated with these genes. These results suggest that active tameness was hidden in the control groups but became apparent in the selected populations by selective breeding, potentially driven by changes in gene expression networks.

Maternal human habituation enhances sons' risk of human-caused mortality in a large carnivore, brown bears

Human habituation of large carnivores is becoming a serious problem that generates human-wildlife conflict, which often results in the removal of animals as nuisances. Although never tested, human habituation potentially reduces the fitness of adult females by reducing their offspring's survival as well as their own, due to an increased likelihood of human-caused mortality. Here, we tested this hypothesis in brown bears inhabiting Shiretoko National Park, Japan. We estimated the frequency of human-caused mortality of independent young (aged 1-4 years) born to mothers living in areas with different maternal levels of human habituation and different proximities to areas of human activity. The overall mortality rate was higher in males than in females, and in females living near a town than those in a remote area of park. Surprisingly, more than 70% of males born to highly habituated mothers living around a remote wildlife protection area were killed by humans; this proportion is greater than that for males born to less-habituated mothers living in almost the same area. The current study clarified that interactions among maternal human habituation, birthplace (proximity to town), age, and sex determine the likelihood of human-caused mortality of brown bears at an early stage of life.

Rapid behavioral assay using handling test provides breed and sex differences in tameness of chickens

BACKGROUND

Japanese indigenous chicken breeds are often used to improve meat quality rather than broilers in the Jidori industry. There are sometimes severe crowding accidents caused by many birds frightened by environmental stimuli. To prevent the economic loss, the chickens need to be more gentle, tame, and imperturbable.

METHODS

In this study, a new handling test for tameness in adult chickens in individual cages was performed with 100 birds from each sex of Shamo, Rhode Island Red, Nagoya, Australorp, and Ukokkei, as well as 10 hens of F1 hybrid between Shamo and Rhode Island Red, to measure both active and passive tameness. We counted the number heading toward human hands (heading) and retreating in other directions (avoiding) in both active and passive tameness phases, as well as the number of steps taken (step) during the handling test.

RESULTS

Male chickens exhibited higher avoidance behavior than females. Nagoya females displayed the lowest level of avoidance behavior, which implies passive tameness. In terms of active tameness, a variety of phenotypes can be obtained in different combinations of breed and sex. These results suggested the handling test will be good method for rapid screening of individual differences in tameness. In addition, there were heterosis effects on avoidance and locomotive behaviors. Since F1 is often used in the Jidori industry, the breeders should be tested not only for meat production but also for tameness.

CONCLUSIONS

In the future, combining both the behavioral screening and the population genomics will establish typical evidence about mechanisms of tameness and domestication in animals.

Changes to social feeding behaviors are not sufficient for fitness gains of the Caenorhabditis elegans N2 reference strain

The standard reference Caenorhabditis elegans strain, N2, has evolved marked behavioral changes in social feeding behavior since its isolation from the wild. We show that the causal, laboratory-derived mutations in two genes, npr-1 and glb-5, confer large fitness advantages in standard laboratory conditions. Using environmental manipulations that suppress social/solitary behavior differences, we show the fitness advantages of the derived alleles remained unchanged, suggesting selection on these alleles acted through pleiotropic traits. Transcriptomics, developmental timing, and food consumption assays showed that N2 animals mature faster, produce more sperm, and consume more food than a strain containing ancestral alleles of these genes regardless of behavioral strategies. Our data suggest that the pleiotropic effects of glb-5 and npr-1 are a consequence of changes to O₂ -sensing neurons that regulate both aerotaxis and energy homeostasis. Our results demonstrate how pleiotropy can lead to profound behavioral changes in a popular laboratory model.

Why do humans walk on two feet? And what makes us smarter than our ape ancestors? The answers to these questions, and countless others about the particular traits of any number of species, is often said to be natural selection – a process where genes that ensure the survival of a species are favored of others. But it is not always the answer. Other evolutionary forces, such as random changes to the frequency of certain gene variants, restrictions on the development of a certain trait and pleiotropy (where one gene influences other, seemingly unrelated traits) can also cause differences between species.

Designing experiments to test whether a trait difference is due to natural selection or other factors is notoriously difficult. However, the humble nematode worm, Caenorhabditis elegans, has proven to be particularly useful in this respect. One subtype or strain of C. elegans with certain changes to its genes is used internationally as a ‘reference strain’, to ensure results between labs are comparable. This strain, N2, has been bred in the laboratory for hundreds of generations, isolated from its wild counterparts. N2 shows several differences in behavior from the wildtype, including its feeding habits. Wild C. elegans tend to feed together socially, whereas N2 prefers to feed alone.

In 1998 and 2009, researchers – including some involved in the current study – have identified the genetic modifications responsible for this change in behavior. Now, Zhao et al. set out to determine whether this was due to natural selection, and if so, was there a benefit to solitary feeding in laboratory conditions that was driving this genetic change? Zhao et al. found that the genetic changes in the N2 strain gave the worms a considerable advantage in the artificial environment. However, experiments to modify the conditions the animals grew in revealed that the solitary feeding habits were not necessary for the fitness advantage. In other words, the changes in feeding habits were a symptom of the genetic changes that gave N2 a selective advantage, but they were not the cause. In other words, the changes in feeding behavior were not a result of natural selection, but rather of pleiotropy.

The findings highlight that not every change in a trait is down to natural selection and must therefore be put to the test. With declining costs of DNA sequencing, researchers can now easily identify genes and regions of DNA that are likely to be under selection. However, they must be careful before leaping to the conclusion that behavioral differences linked to genetic changes are adaptive. In addition, the findings show that the laboratories relying on N2 as a model organism should be aware that the strain has evolved fundamental differences in its brain connections compared with the wildtype.

Measuring Active and Passive Tameness Separately in Mice

Domesticated animals such as dogs and laboratory mice show a high level of tameness, which is important for humans to handle them easily. Tameness has two behavioral components: a reluctance to avoid humans (passive tameness) and a motivation to approach humans (active tameness). To quantify these components in mice, we previously developed behavioral tests for active tameness, passive tameness, and the willingness to stay on a human hand, each designed to be completed within 3 min. The data obtained were used for selective breeding, with a large number of mice analyzed per generation. The active tameness test measures the movement of the mouse toward a human hand and the contact it engages in. The passive tameness test measures the duration of time that a mouse tolerates human touch. In the stay-on-hand test, a mouse is placed on a human hand and touched slowly using the thumb of that hand; the duration of time that the animal remains on the hand is measured. Here, we describe the test set-up and apparatus, explain the procedures, and discuss the appropriate data analysis. Finally, we explain how to interpret the results.

Tunnel use facilitates handling of ICR mice and decreases experimental variation

We evaluated a handling method using tunnels to tame laboratory mice (ICR) in the context of animal welfare and ease of handling. During 1-week acclimation to handling and subsequent 1-week oral administration (once per day), voluntary interaction with the experimenter was much greater in mice handled by a tunnel compared to those picked up by the tail. According to a rating of the ease of handling laboratory mice, a tunnel facilitated mouse handling during acclimation to handling and oral gavage of saline compared to tail handling. In addition, mice handled by a tunnel showed less anxiety than mice handled by the tail in the open field test, but not in elevated plus maze. Calculation of experimental variation in behavioral tests, which were used to mimic pharmacological studies, suggested that mice handled by a tunnel exhibited the tendency of less variation compared to those picked up by the tail, in both groups that were intraperitoneally administered saline as placebo and diazepam as an active drug. Thus, tunnel use could be beneficial for improving animal welfare and facilitated handling of ICR mice in mouse studies.

A longitudinal study of phenotypic changes in early domestication of house mice

Similar phenotypic changes occur across many species as a result of domestication, e.g. in pigmentation and snout size. Experimental studies of domestication have concentrated on intense and directed selection regimes, while conditions that approximate the commensal and indirect interactions with humans have not been explored. We examine long-term data on a free-living population of wild house mice that have been indirectly selected for tameness by regular exposure to humans. In the course of a decade, this mouse population exhibited significantly increased occurrence of white patches of fur and decreased head length. These phenotypic changes fit to the predictions of the 'domestication syndrome'.

Effects of Strain and Species on the Septo-Temporal Distribution of Adult Neurogenesis in Rodents

The functional septo-temporal (dorso-ventral) differentiation of the hippocampus is accompanied by gradients of adult hippocampal neurogenesis (AHN) in laboratory rodents. An extensive septal AHN in laboratory mice suggests an emphasis on a relation of AHN to tasks that also depend on the septal hippocampus. Domestication experiments indicate that AHN dynamics along the longitudinal axis are subject to selective pressure, questioning if the septal emphasis of AHN in laboratory mice is a rule applying to rodents in general. In this study, we used C57BL/6 and DBA2/Crl mice, wild-derived F1 house mice and wild-captured wood mice and bank voles to look for evidence of strain and species specific septo-temporal differences in AHN. We confirmed the septal > temporal gradient in C57BL/6 mice, but in the wild species, AHN was low septally and high temporally. Emphasis on the temporal hippocampus was particularly strong for doublecortin positive (DCX+) young neurons and more pronounced in bank voles than in wood mice. The temporal shift was stronger in female wood mice than in males, while we did not see sex differences in bank voles. AHN was overall low in DBA and F1 house mice, but they exhibited the same inversed gradient as wood mice and bank voles. DCX+ young neurons were usually confined to the subgranular zone and deep granule cell layer. This pattern was seen in all animals in the septal and intermediate dentate gyrus. In bank voles and wood mice however, the majority of temporal DCX+ cells were radially dispersed throughout the granule cell layer. Some but not all of the septo-temporal differences were accompanied by changes in the DCX+/Ki67+ cell ratios, suggesting that new neuron numbers can be regulated by both proliferation or the time course of maturation and survival of young neurons. Some of the septo-temporal differences we observe have also been found in laboratory rodents after the experimental manipulation of the molecular mechanisms that control AHN. Adaptations of AHN under natural conditions may operate on these or similar mechanisms, adjusting neurogenesis to the requirements of hippocampal function.

Hierarchy in the home cage affects behaviour and gene expression in group-housed C57BL/6 male mice

Group-housed male mice exhibit aggressive behaviour towards their cage mates and form a social hierarchy. Here, we describe how social hierarchy in standard group-housed conditions affects behaviour and gene expression in male mice. Four male C57BL/6 mice were kept in each cage used in the study, and the social hierarchy was determined from observation of video recordings of aggressive behaviour. After formation of a social hierarchy, the behaviour and hippocampal gene expression were analysed in the mice. Higher anxiety- and depression-like behaviours and elevated gene expression of hypothalamic corticotropin-releasing hormone and hippocampal serotonin receptor subtypes were observed in subordinate mice compared with those of dominant mice. These differences were alleviated by orally administering fluoxetine, which is an antidepressant of the selective serotonin reuptake inhibitor class. We concluded that hierarchy in the home cage affects behaviour and gene expression in male mice, resulting in anxiety- and depression-like behaviours being regulated differently in dominant and subordinate mice.

Selective breeding and selection mapping using a novel wild-derived heterogeneous stock of mice revealed two closely-linked loci for tameness

Tameness is a major behavioral factor for domestication, and can be divided into two potential components: motivation to approach humans (active tameness) and reluctance to avoid humans (passive tameness). We identified genetic loci for active tameness through selective breeding, selection mapping, and association analysis. In previous work using laboratory and wild mouse strains, we found that laboratory strains were predominantly selected for passive tameness but not active tameness during their domestication. To identify genetic regions associated with active tameness, we applied selective breeding over 9 generations for contacting, a behavioural parameter strongly associated with active tameness. The prerequisite for successful selective breeding is high genetic variation in the target population, so we established and used a novel resource, wild-derived heterogeneous stock (WHS) mice from eight wild strains. The mice had genetic variations not present in other outbred mouse populations. Selective breeding of the WHS mice increased the contacting level through the generations. Selection mapping was applied to the selected population using a simulation based on a non-selection model and inferred haplotype data derived from single-nucleotide polymorphisms. We found a genomic signature for selection on chromosome 11 containing two closely linked loci.

CRISPR/Cas9-mediated genome editing in wild-derived mice: generation of tamed wild-derived strains by mutation of the a (nonagouti) gene

Wild-derived mice have contributed to experimental mouse genetics by virtue of their genetic diversity, which may help increase the chance of identifying novel modifier genes responsible for specific phenotypes and diseases. However, gene targeting using wild-derived mice has been unsuccessful because of the unavailability of stable embryonic stem cells. Here, we report that CRISPR/Cas9-mediated gene targeting can be applied to the Japanese wild-derived MSM/Ms strain (Mus musculus molossinus). We targeted the nonagouti (a) gene encoding the agouti protein that is localized in hair and the brain. We obtained three homozygous knockout mice as founders, all showing black coat colour. While homozygous knockout offspring were physiologically indistinguishable from wild-type litter-mates, they showed specific domesticated behaviours: hypoactivity in the dark phase and a decline in the avoidance of a human hand. These phenotypes were consistent over subsequent generations. Our findings support the empirical hypothesis that nonagouti is a domestication-linked gene, the loss of which might repress aggressive behaviour.

Genomic signatures of domestication on neurogenetic genes in Drosophila melanogaster

BACKGROUND

Domesticated animals quickly evolve docile and submissive behaviors after isolation from their wild conspecifics. Model organisms reared for prolonged periods in the laboratory also exhibit similar shifts towards these domesticated behaviors. Yet whether this divergence is due to inadvertent selection in the lab or the fixation of deleterious mutations remains unknown.

RESULTS

Here, we compare the genomes of lab-reared and wild-caught Drosophila melanogaster to understand the genetic basis of these recently endowed behaviors common to laboratory models. From reassembled genomes of common lab strains, we identify unique, derived variants not present in global populations (lab-specific SNPs). Decreased selective constraints across low frequency SNPs (unique to one or two lab strains) are different from patterns found in the wild and more similar to neutral expectations, suggesting an overall accumulation of deleterious mutations. However, high-frequency lab SNPs found in most or all lab strains reveal an enrichment of X-linked loci and neuro-sensory genes across large extended haplotypes. Among shared polymorphisms, we also find highly differentiated SNPs, in which the derived allele is higher in frequency in the wild (Fst*wild>lab), enriched for similar neurogenetic ontologies, indicative of relaxed selection on more active wild alleles in the lab.

CONCLUSIONS

Among random mutations that continuously accumulate in the laboratory, we detect common adaptive signatures in domesticated lab strains of fruit flies. Our results demonstrate that lab animals can quickly evolve domesticated behaviors via unconscious selection by humans early on a broad pool of disproportionately large neurogenetic targets followed by the fixation of accumulated deleterious mutations on functionally similar targets.

Genetic mapping of escalated aggression in wild-derived mouse strain MSM/Ms: association with serotonin-related genes

The Japanese wild-derived mouse strain MSM/Ms (MSM) retains a wide range of traits related to behavioral wildness, including high levels of emotionality and avoidance of humans. In this study, we observed that MSM showed a markedly higher level of aggression than the standard laboratory strain C57BL/6J. Whereas almost all MSM males showed high frequencies of attack bites and pursuit in the resident-intruder test, only a few C57BL/6J males showed aggressive behaviors, with these behaviors observed at only a low frequency. Sexually mature MSM males in their home cages killed their littermates, or sometimes female pair-mates. To study the genetic and neurobiological mechanisms that underlie the escalated aggression observed in MSM mice, we analyzed reciprocal F1 crosses and five consomic strains of MSM (Chr 4, 13, 15, X and Y) against the background of C57BL/6J. We identified two chromosomes, Chr 4 and Chr 15, which were involved in the heightened aggression observed in MSM. These chromosomes had different effects on aggression: whereas MSM Chr 15 increased agitation and initiation of aggressive events, MSM Chr 4 induced a maladaptive level of aggressive behavior. Expression analysis of mRNAs of serotonin receptors, serotonin transporter and Tph2, an enzyme involved in serotonin synthesis in seven brain areas, indicated several differences among MSM, C57BL/6J, and their consomic strains. We found that Tph2 expression in the midbrain was increased in the Chr 4 consomic strain, as well as in MSM, and that there was a strong positive genetic correlation between aggressive behavior and Tph2 expression at the mRNA level. Therefore, it is possible that increased expression of the Tph2 gene is related to escalated aggression observed in MSM.