Tracking the Near Eastern origins and European dispersal of the western house mouse

Pests or prey? Micromammal species within an ancient anthropic environment at the Norse settlement site of Tuquoy (Westray, Orkney)

Micromammals, like rodents and shrews, adapt rapidly to take advantage of new food sources, habitats and ecological niches, frequently thriving in anthropogenic environments. Their remains, often retrieved during archaeological investigations, can be a valuable source of information about the past environmental conditions as well as interspecies interactions and human activity. However, the research on such finds rarely covers multiple approaches, often relying on single species or data type (e.g. identification/information for proxy studies). Here we investigate micromammal remains from the Norse and medieval (AD tenth-fourteenth centuries) archaeological site at Tuquoy, Orkney, to elucidate the relationships between micromammals, humans and other species present using a variety of data. Four micromammal species were identified, and their species dynamics as well as relationships with humans could be inferred by tracking changes in spatial and temporal location of remains, from their taphonomic history and by age estimation for individual animals. A larger, predatory assemblage was also identified, with species composition differing from that in the rest of the archaeological assemblage, and possibly therefore representing small mammal species composition in the wild. The assemblage was probably deposited by a diurnal raptor, though identification to species is not certain due to post-depositional processes.

The demographic history of house mice (Mus musculus domesticus) in eastern North America

The Western European house mouse (Mus musculus domesticus) is a widespread human commensal that has recently been introduced to North America. Its introduction to the Americas is thought to have resulted from the transatlantic movements of Europeans that began in the early 16th century. To study the details of this colonization history, we examine population structure, explore relevant demographic models, and infer the timing of divergence among house mouse populations in the eastern United States using published exome sequences from five North American populations and two European populations. For North American populations of house mice, levels of nucleotide variation were lower, and low-frequency alleles were less common than for European populations. These patterns provide evidence of a mild bottleneck associated with the movement of house mice into North America. Several analyses revealed that one North American population is genetically admixed, which indicates at least two source populations from Europe were independently introduced to eastern North America. Estimated divergence times between North American and German populations ranged between ∼1,000 and 7,000 years ago and overlapped with the estimated divergence time between populations from Germany and France. Demographic models comparing different North American populations revealed that these populations diverged from each other mostly within the last 500 years, consistent with the timing of the arrival of Western European settlers to North America. Together, these results support a recent introduction of Western European house mice to eastern North America, highlighting the effects of human migration and colonization on the spread of an invasive human commensal.

Environmental implications of Ptolemaic Period rodents and shrews from the Sacred Falcon Necropolis at Quesna, Egypt (Mammalia: Muridae and Soricidae)

BACKGROUND

Assemblages of mummified and preserved animals in necropoleis of Ptolemaic Period Egypt (ca. 332-30 BC) document some aspects of the ceremonial and religious practices of the ancient Egyptians, but study of these animal remains can also provide insight into the local environments in which the animals and humans lived.

RESULTS

Excavations of the Sacred Falcon Necropolis at Quesna in the Nile Delta have yielded many thousands of animal remains, mostly of raptors, but also of a lesser number of small, wild mammals. Among the latter, we identified four species of murid rodents (Rodentia: Muridae) and five species of shrews (Eulipotyphla: Soricidae). The soricids are of particular interest because they represent a more diverse assemblage of species than occurs in the delta today. They include one species, Crocidura gueldenstaedtii (Pallas, 1811), that no longer occurs in the delta and another, C. fulvastra (Sundevall, 1843), that is now extirpated from Egypt.

CONCLUSIONS

The coexistence of this diverse small mammal community suggests that a greater availability and variety of mesic habitats were present during the Ptolemaic Period than occur there now. The local mammal faunas recovered at Quesna and other well-studied ancient Egyptian sites together provide evidence of a richer, more complex regional environment along the Nile Valley. They also provide important insight regarding the biogeography of the individual species comprising the faunas and about the extent of faunal turnover since the Ptolemaic Period.

Genetics of randomly bred cats support the cradle of cat domestication being in the Near East

Cat domestication likely initiated as a symbiotic relationship between wildcats (Felis silvestris subspecies) and the peoples of developing agrarian societies in the Fertile Crescent. As humans transitioned from hunter-gatherers to farmers ~12,000 years ago, bold wildcats likely capitalized on increased prey density (i.e., rodents). Humans benefited from the cats' predation on these vermin. To refine the site(s) of cat domestication, over 1000 random-bred cats of primarily Eurasian descent were genotyped for single-nucleotide variants and short tandem repeats. The overall cat population structure suggested a single worldwide population with significant isolation by the distance of peripheral subpopulations. The cat population heterozygosity decreased as genetic distance from the proposed cat progenitor's (F.s. lybica) natural habitat increased. Domestic cat origins are focused in the eastern Mediterranean Basin, spreading to nearby islands, and southernly via the Levantine coast into the Nile Valley. Cat population diversity supports the migration patterns of humans and other symbiotic species.

Population structure and inbreeding in wild house mice (Mus musculus) at different geographic scales

House mice (Mus musculus) have spread globally as a result of their commensal relationship with humans. In the form of laboratory strains, both inbred and outbred, they are also among the most widely used model organisms in biomedical research. Although the general outlines of house mouse dispersal and population structure are well known, details have been obscured by either limited sample size or small numbers of markers. Here we examine ancestry, population structure, and inbreeding using SNP microarray genotypes in a cohort of 814 wild mice spanning five continents and all major subspecies of Mus, with a focus on M. m. domesticus. We find that the major axis of genetic variation in M. m. domesticus is a south-to-north gradient within Europe and the Mediterranean. The dominant ancestry component in North America, Australia, New Zealand, and various small offshore islands are of northern European origin. Next we show that inbreeding is surprisingly pervasive and highly variable, even between nearby populations. By inspecting the length distribution of homozygous segments in individual genomes, we find that inbreeding in commensal populations is mostly due to consanguinity. Our results offer new insight into the natural history of an important model organism for medicine and evolutionary biology.

Stable isotopes unveil one millennium of domestic cat paleoecology in Europe

The domestic cat is the world's most popular pet and one of the most detrimental predators in terrestrial ecosystems. Effective protection of wildlife biodiversity demands detailed tracking of cat trophic ecology, and stable isotopes serve as a powerful proxy in dietary studies. However, a variable diet can make an isotopic pattern unreadable in opportunistic predators. To evaluate the usefulness of the isotopic method in cat ecology, we measured C and N isotope ratios in hundreds of archaeological cat bones. We determined trends in cat trophic paleoecology in northern Europe by exploiting population-scale patterns in animals from diverse locations. Our dataset shows a high variability of isotopic signals related to the socio-economic and/or geomorphological context. This points toward regularities in isotopic patterns across past cat populations. We provide a generalized guide to interpret the isotopic ecology of cats, emphasizing that regional isotopic baselines have a major impact on the isotopic signal.

Small Animals, Big Impact? Early Farmers and Pre- and Post-Harvest Pests from the Middle Neolithic Site of Les Bagnoles in the South-East of France (L’Isle-sur-la-Sorgue, Vaucluse, Provence-Alpes-Côte-d’Azur)

Pests appear to have accompanied humans and their crops since the beginning of farming. Nevertheless, their study is only rarely integrated into research on farming in prehistory. An assemblage of invertebrates and small mammals was recovered from the waterlogged layers of three wells at the Middle Neolithic site (4250–3700 cal B.C.) of Les Bagnoles (SE France). The microfaunal remains were retrieved from sediment samples by wet sieving (wash-over technique). The most common among the rodents is the wood mouse. The assemblage also consists of insect remains of grain weevil, seed beetle, and corn ground beetle. The different finds not only offer data on the role of insect and rodent pests in the Neolithic but on the possible strategies adopted by the early farming communities in the western Mediterranean in response to pest infestation. The findings appear to confirm the hypothesis that the wood mouse was a commensal and storage pest in settlements long before the arrival of the invasive house mouse during the Bronze Age. The presence of the main storage pest, the grain weevil, suggests a long-term grain storage issue at Les Bagnoles. The combination of the results of the site’s archaeobotanical findings with those of other sites in the western Mediterranean suggests that the shift from naked to glume wheat around 4000 B.C. may also stem from a reaction to the problem of grain weevil infestation.

The Global and Western Indian Ocean Dispersal of House Geckos From Asia Using Historical and Mitochondrial DNA Perspectives

Seven species of house geckos occur across the scattered islands of the Indian Ocean. Two of these, Hemidactylus frenatus and H. parvimaculatus are both widespread and possess distribution profiles that suggest pre-European, or perhaps natural dispersal to some islands. Of these, only H. frenatus currently has sufficient molecular data to begin exploring dispersal patterns. This species is one of the most successful reptile colonists, as demonstrated by its global, pantropical distribution. While in some areas, such as Australia and continental South America, its dispersal patterns are both recent and well-known, early historical records of Hemidactylus in the Indian Ocean islands suggest earlier and/or potentially non-human-mediated dispersals. Here, we reviewed the historical literature and combined those reports with an assessment of mitochondrial DNA diversity of a global sampling of H. frenatus samples that included modern and museum specimens. Our results corroborate previous studies and demonstrate the relatively high diversity within this species’ native range in Southeast Asia. In addition, the phylogenetic analysis suggests both a potential cryptic species complex, as well as global geographic structuring of different H. frenatus mitochondrial lineages. This has important implications for many comparative studies of this complex. Frequent and ongoing dispersals and colonizations complicate the identification of potentially older migration patterns. Further assessments including additional samples and analyses of additional genetic markers are necessary to disentangle older from more recent dispersals within this intriguing species.

What is domestication?

The nature of domestication is often misunderstood. Most definitions of the process are anthropocentric and center on human intentionality, which minimizes the role of unconscious selection and also excludes non-human domesticators. An overarching, biologically grounded definition of domestication is discussed, which emphasizes its core nature as a coevolutionary process that arises from a specialized mutualism, in which one species controls the fitness of another in order to gain resources and/or services. This inclusive definition encompasses both human-associated domestication of crop plants and livestock as well as other non-human domesticators, such as insects. It also calls into question the idea that humans are themselves domesticated, given that evolution of human traits did not arise through the control of fitness by another species.

Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we first generate a de novo genome assembly of the black rat. We then sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of our newly reported sequences, together with published mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.

‘Archaeogenetic analysis of black rat remains reveals that this species was introduced into temperate Europe twice, in the Roman and medieval periods. This population turnover was likely associated with multiple historical and environmental factors.’

Bidirectional introgression between Mus musculus domesticus and Mus spretus

Introgressed variants from other species can be an important source of genetic variation because they may arise rapidly, can include multiple mutations on a single haplotype, and have often been pretested by selection in the species of origin. Although introgressed alleles are generally deleterious, several studies have reported introgression as the source of adaptive alleles—including the rodenticide-resistant variant of Vkorc1 that introgressed from Mus spretus into European populations of Mus musculus domesticus. Here, we conducted bidirectional genome scans to characterize introgressed regions into one wild population of M. spretus from Spain and three wild populations of M. m. domesticus from France, Germany, and Iran. Despite the fact that these species show considerable intrinsic postzygotic reproductive isolation, introgression was observed in all individuals, including in the M. musculus reference genome (GRCm38). Mus spretus individuals had a greater proportion of introgression compared with M. m. domesticus, and within M. m. domesticus, the proportion of introgression decreased with geographic distance from the area of sympatry. Introgression was observed on all autosomes for both species, but not on the X-chromosome in M. m. domesticus, consistent with known X-linked hybrid sterility and inviability genes that have been mapped to the M. spretus X-chromosome. Tract lengths were generally short with a few outliers of up to 2.7 Mb. Interestingly, the longest introgressed tracts were in olfactory receptor regions, and introgressed tracts were significantly enriched for olfactory receptor genes in both species, suggesting that introgression may be a source of functional novelty even between species with high barriers to gene flow.

The Microvertebrates of Shanidar Cave: Preliminary Taphonomic Findings

Shanidar Cave, Iraqi Kurdistan, is one of the most important Palaeolithic sites in Southwest Asia. This is due to the long sequence of hominin occupation of the cave and the discovery of multiple Neanderthal individuals from the original Solecki excavations (1951–1960) and recent excavations (2014 to present). Preliminary taphonomic analyses of the microvertebrate assemblage were undertaken to understand the factors affecting assemblage formation and accumulation, and this paper presents the first results of these analyses. All contexts display a high proportion of fragmentation, with a slight decrease in breakage towards the base of the sequence. Black staining and root etching were observed in a similar pattern, present in most contexts but with an increase in the lower levels. A significant proportion of the microvertebrate remains examined displayed light traces of digestion, indicating some contribution to the assemblage by predators. The results are consistent with wider palaeoecological records that indicate relatively warm, wet conditions at the base of the sequence and cooler, drier conditions at the top.

Selection shapes the landscape of functional variation in wild house mice

BACKGROUND

Through human-aided dispersal over the last ~ 10,000 years, house mice (Mus musculus) have recently colonized diverse habitats across the globe, promoting the emergence of new traits that confer adaptive advantages in distinct environments. Despite their status as the premier mammalian model system, the impact of this demographic and selective history on the global patterning of disease-relevant trait variation in wild mouse populations is poorly understood.

RESULTS

Here, we leveraged 154 whole-genome sequences from diverse wild house mouse populations to survey the geographic organization of functional variation and systematically identify signals of positive selection. We show that a significant proportion of wild mouse variation is private to single populations, including numerous predicted functional alleles. In addition, we report strong signals of positive selection at many genes associated with both complex and Mendelian diseases in humans. Notably, we detect a significant excess of selection signals at disease-associated genes relative to null expectations, pointing to the important role of adaptation in shaping the landscape of functional variation in wild mouse populations. We also uncover strong signals of selection at multiple genes involved in starch digestion, including Mgam and Amy1. We speculate that the successful emergence of the human-mouse commensalism may have been facilitated, in part, by dietary adaptations at these loci. Finally, our work uncovers multiple cryptic structural variants that manifest as putative signals of positive selection, highlighting an important and under-appreciated source of false-positive signals in genome-wide selection scans.

CONCLUSIONS

Overall, our findings highlight the role of adaptation in shaping wild mouse genetic variation at human disease-associated genes. Our work also highlights the biomedical relevance of wild mouse genetic diversity and underscores the potential for targeted sampling of mice from specific populations as a strategy for developing effective new mouse models of both rare and common human diseases.

Using Free-Range Laboratory Mice to Explore Foraging, Lifestyle, and Diet Issues in Cancer

As cancer progresses, its impact should manifest in the foraging behavior of its host much like the effects of endo-parasites that hinder foraging aptitudes and risk management abilities. Furthermore, the lifestyle of the host can impact tumor growth and quality of life. To approach these questions, we conducted novel experiments by letting C57BL/6 laboratory mice, with or without oral squamous cell carcinoma, free range in a large outdoor vivarium. Our goals were to: (1) determine whether one could conduct experiments with a mouse model under free range conditions, (2) measure effects of cancer burden on foraging metrics, (3) compare tumor growth rates with laboratory housed mice, and (4) begin to sort out confounding factors such as diet. With or without cancer, the C57BL/6 laboratory mice dealt with natural climatic conditions and illumination, found shelter or dug burrows, sought out food from experimental food patches, and responded to risk factors associated with microhabitat by foraging more thoroughly in food patches under bush (safe) than in the open (risky). We quantified foraging using giving-up densities of food left behind in the food patches. The mice’s patch use changed over time, and was affected by disease status, sex, and microhabitat. Males, which were larger, consumed more food and had lower giving-up densities than females. Relative to cancer-free mice, mice with growing tumors lost weight, harvested more food, and increasingly relied on patches in the bush microhabitat. The tumors of free-ranging mice in the vivarium grew slower than those of their cohort that were housed in mouse cages in animal facilities. Numerous interesting factors could explain the difference in tumor growth rates: activity levels, stress, weather, food intake, diet, and more. To tease apart one of these intertwined factors, we found that tumors grew faster when mice in the laboratory were fed on millet rather than laboratory mouse chow. While just a start, these novel experiments and framework show how free-ranging mice provide a model that can test a broader range of hypotheses and use a broader range of metrics regarding cancer progression and its consequences for the host.

Patterns of Coevolutionary Adaptations across Time and Space in Mouse Gammaretroviruses and Three Restrictive Host Factors

The classical laboratory mouse strains are genetic mosaics of three Mus musculus subspecies that occupy distinct regions of Eurasia. These strains and subspecies carry infectious and endogenous mouse leukemia viruses (MLVs) that can be pathogenic and mutagenic. MLVs evolved in concert with restrictive host factors with some under positive selection, including the XPR1 receptor for xenotropic/polytropic MLVs (X/P-MLVs) and the post-entry restriction factor Fv1. Since positive selection marks host-pathogen genetic conflicts, we examined MLVs for counter-adaptations at sites that interact with XPR1, Fv1, and the CAT1 receptor for ecotropic MLVs (E-MLVs). Results describe different co-adaptive evolutionary paths within the ranges occupied by these virus-infected subspecies. The interface of CAT1, and the otherwise variable E-MLV envelopes, is highly conserved; antiviral protection is afforded by the Fv4 restriction factor. XPR1 and X/P-MLVs variants show coordinate geographic distributions, with receptor critical sites in envelope, under positive selection but with little variation in envelope and XPR1 in mice carrying P-ERVs. The major Fv1 target in the viral capsid is under positive selection, and the distribution of Fv1 alleles is subspecies-correlated. These data document adaptive, spatial and temporal, co-evolutionary trajectories at the critical interfaces of MLVs and the host factors that restrict their replication.

New insights into the spatial organization, stratigraphy and human occupations of the Aceramic Neolithic at Ganj Dareh, Iran

The Aceramic Neolithic site of Ganj Dareh (Kermanshah, Iran) is arguably one of the most significant sites for enhancing our understanding of goat domestication and the onset of sedentism. Despite its central importance, it has proven difficult to obtain contextually reliable data from it and integrate the site in regional syntheses because it was never published in full after excavations ceased in 1974. This paper presents the Ganj Dareh archive at Université de Montréal and shows how the documentation and artifacts it comprises still offer a great deal of useful information about the site. In particular, we 1) present the first stratigraphic profile for the site, which reveals a more complex depositional history than Smith's five-level sequence; 2) reveal the presence of two possible pre-agricultural levels (H-01 and P-01); 3) explore the spatial organization of different levels; 4) explain possible discrepancies in the radiocarbon dates from the site; 5) show some differences in lithic technological organization in levels H-01 and P-01 suggestive of higher degrees of residential mobility than subsequent phases of occupation at the site; and 6) reanalyze the burial data to broaden our understanding of Aceramic Neolithic mortuary practices in the Zagros. These data help refine our understanding of Ganj Dareh's depositional and occupational history and recenter it as a key site to improve our understanding the Neolithization process in the Middle East.

Bones geometric morphometrics illustrate 10th millennium cal. BP domestication of autochthonous Cypriot wild boar (Sus scrofa circeus nov. ssp)

Epipaleolithic hunter-gatherers from the Near East introduced wild boars (Sus scrofa) to Cyprus, with the Early Pre-Pottery Neolithic (PPN) settlers hunting the wild descendants of these boars. However, the geographic origin of the Cypriot boar and how they were integrated into the earliest forms of pig husbandry remain unsolved. Here, we present data on 11,000 to 9000 cal. BP Sus scrofa from the PPN sites of Klimonas and Shillourokambos. We compared them to contemporaneous populations from the Near East and to Neolithic and modern populations in Corsica, exploring their origin and evolution using biosystematic signals from molar teeth and heel bones (calcanei), using 2D and 3D geometric morphometrics. We found that the Cypriot PPN lineage of Sus scrofa originates from the Northern Levant. Yet, their phenotypic idiosyncrasy suggest that they evolved into an insular sub-species that we named Sus scrofa circeus, referring to Circe, the metamorphosis goddess that changed Ulysses companions into pigs. The phenotypic homogeneity among PPNA Klimonas wild boars and managed populations of PPNB Shillourokambos suggests that local domestication has been undertaken on the endemic S. s. circeus, strengthening the idea that Cyprus was integrated into the core region of animal domestication.

The mutational load in natural populations is significantly affected by high primary rates of retroposition

The phenomenon of retroposition (the reintegration of reverse-transcribed RNA into the genome) has been well studied in comparisons between species and has been identified as a source of evolutionary innovation. However, less attention has been paid to possible negative effects of retroposition. To trace the evolutionary dynamics of these negative effects, our study uses a unique genomic dataset of house mouse populations. It reveals that the initial retroposition rate is very high and that most of these newly transposed retrocopies have a deleterious impact, apparently through modifying the expression of their parental genes. In humans, this effect is expected to cause disease alleles, and we propose that genetic screening should include the search for newly transposed retrocopies.

Gene retroposition is known to contribute to patterns of gene evolution and adaptations. However, possible negative effects of gene retroposition remain largely unexplored since most previous studies have focused on between-species comparisons where negatively selected copies are mostly not observed, as they are quickly lost from populations. Here, we show for natural house mouse populations that the primary rate of retroposition is orders of magnitude higher than the long-term rate. Comparisons with single-nucleotide polymorphism distribution patterns in the same populations show that most retroposition events are deleterious. Transcriptomic profiling analysis shows that new retroposed copies become easily subject to transcription and have an influence on the expression levels of their parental genes, especially when transcribed in the antisense direction. Our results imply that the impact of retroposition on the mutational load has been highly underestimated in natural populations. This has additional implications for strategies of disease allele detection in humans.

Ancient mitochondrial DNA connects house mice in the British Isles to trade across Europe over three millennia

Background

The earliest records in Britain for the western European house mouse (Mus musculus domesticus) date from the Late Bronze Age. The arrival of this commensal species in Britain is thought to be related to human transport and trade with continental Europe. In order to study this arrival, we collected a total of 16 ancient mouse mandibulae from four early British archaeological sites, ranging from the Late Bronze Age to the Roman period.

Results

From these, we obtained ancient mitochondrial DNA (mtDNA) house mouse sequences from eight house mice from two of the sites dating from the Late Bronze to Middle Iron Age. We also obtained five ancient mtDNA wood mouse (Apodemus spp.) sequences from all four sites. The ancient house mouse sequences found in this study were from haplogroups E (N = 6) and D (N = 2). Modern British house mouse mtDNA sequences are primarily characterised by haplogroups E and F and, much less commonly, haplogroup D.

Conclusions

The presence of haplogroups D and E in our samples and the dating of the archaeological sites provide evidence of an early house mouse colonisation that may relate to Late Bronze Age/Iron Age trade and/or human expansion. Our results confirm the hypothesis, based on zooarchaeological evidence and modern mtDNA predictions, that house mice, with haplogroups D and E, were established in Britain by the Iron Age and, in the case of haplogroup E, possibly as early as the Late Bronze Age.

Genetic structure in Orkney island mice: isolation promotes morphological diversification

Following human occupation, the house mouse has colonised numerous islands, exposing the species to a wide variety of environments. Such a colonisation process, involving successive founder events and bottlenecks, may either promote random evolution or facilitate adaptation, making the relative importance of adaptive and stochastic processes in insular evolution difficult to assess. Here, we jointly analyse genetic and morphometric variation in the house mice (Mus musculus domesticus) from the Orkney archipelago. Genetic analyses, based on mitochondrial DNA and microsatellites, revealed considerable genetic structure within the archipelago, suggestive of a high degree of isolation and long-lasting stability of the insular populations. Morphometric analyses, based on a quantification of the shape of the first upper molar, revealed considerable differentiation compared to Western European populations, and significant geographic structure in Orkney, largely congruent with the pattern of genetic divergence. Morphological diversification in Orkney followed a Brownian motion model of evolution, suggesting a primary role for random drift over adaptation to local environments. Substantial structuring of human populations in Orkney has recently been demonstrated, mirroring the situation found here in house mice. This synanthropic species may thus constitute a bioproxy of human structure and practices even at a very local scale.