Available online 3 January 2013

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Genetic tracking of mice and other bioproxies to infer human history

• Eleanor P. Jones^{1, 2},
• Heidi M. Eager^{3, 4},
• Sofia I. Gabriel⁵,
• Fríða Jóhannesdóttir⁴,
• Jeremy B. Searle^{1, 4,}

• ¹ Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
• ² Population Biology and Conservation Biology, Evolutionary Biology Centre, University of Uppsala, SE-752 36 Uppsala, Sweden
• ³ Research Laboratory for Archaeology and the History of Art, School of Archaeology, University of Oxford, Oxford OX1 2HU, UK
• ⁴ Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY 14853-2701, USA
• ⁵ Centre for Environmental and Marine Studies (CESAM), Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, 1749–016 Lisbon, Portugal

Available online 3 January 2013

• http://dx.doi.org/10.1016/j.tig.2012.11.011, How to Cite or Link Using DOI

Keywords

• archaeology;
• colonisation history;
• house mouse;
• Mus musculus domesticus;
• phylogeography;
• Vikings

Co-phylogeography of humans and their close associates

Genetic markers can be used to track the colonisation and demographic history of organisms by fitting their genealogies to geographical and temporal frameworks (Box 1). This approach is known as phylogeography and, in the case of more than one organism, ‘comparative’ phylogeography can be used to infer common histories between them [1]. Co-phylogeography, a special case of comparative phylogeography, was first used to describe the intimate linkage between the colonisation and demographic history of an organism and its parasites [2]. Here we extend the term to encompass a wider suite of organisms that, through their close association with humans, share a common colonisation history, including organisms that humans exploit (e.g., plant and animal domesticates) as well as those that exploit humans (e.g., pathogens, parasites, pests). It is by moving these organisms around that humans create a mutual colonisation history.

When genetic analyses of human-associated species do reveal a common history, they can be viewed as historical ‘proxies’ [3], and the phylogeography of these associates may fill in gaps in our knowledge and understanding of human movements and demographic history. It is this potential use of other organisms to tell us about human history that we explore here. We first develop the principles behind the use of ‘bioproxies’ as archaeological tools, and survey examples of them, before examining the house mouse (Mus musculus) as a detailed case-study.

Bioproxies in historical inference

Most of our knowledge about the human past comes from documentary evidence, analysis of material artefacts (Figure 1) and other vestiges of a human lifestyle, and interpretation of human remains. More recently, important insights into the colonisation and demographic histories of humans have been gained from genetic (phylogeographic) studies of both contemporary humans (using modern DNA) and archaeological human remains (using ancient DNA), such as the initial human colonisation of the Americas [4] and the recent colonisation of Scandinavia [5].

Analogous to material artefacts, bioproxies may be considered ‘living artefacts’ – organisms taken to a place and left there by people moving between locations – artefacts with a (potentially enormous) information content dependent on the depth of analysis of the genomes of the organisms. Bioproxy phylogeography may be more valuable than human phylogeography in determining the human colonisation history of an area, for instance in situations where the human colonists and their descendants have left or died out, or if the genetic signal of the original human founders is obscured by subsequent immigration. Bioproxies also avoid ethical concerns of working directly on humans.

The phylogeography of bioproxies may be an alternative or complement to the phylogeography of humans when considering any period from the origin of humans onwards. However, bioproxies become particularly valuable at elucidating human movements after the formation of settled societies, agriculture, and transport [6]. This is when people became closely associated with a large number of different types of organisms and developed an increasingly complex colonisation history brought about by recurrent immigration and emigration, which bioproxies can help to unravel.

Categories of bioproxies

Bioproxies can be divided into three main categories, representing many species used in phylogeographic studies: domesticates (and other purposefully transported organisms), commensals (unintentionally transported organisms), and pathogens and parasites.

Numerous phylogeographic studies on modern and archaeological specimens have investigated the domestication centres for different species and the spread of those domesticates thereafter (e.g., sheep Ovis orientalis[7], cattle Bos primigenius 8 and 9, grape Vitis vinifera[10], and maize Zea mays[11]). These studies reveal not only aspects of the spread of agriculture, but also human migrations by people who carried domesticates with them. This is exemplified by studies on the pig (Sus scrofa), examining the spread of the Neolithic through Europe [12], and human colonisation of Oceania [13]. Care is needed, however, in interpreting genetic data on extant breeds and cultivars [14], because replacement events (humans bringing in new breeds) may wipe out earlier colonisation events, although original colonists may survive in a feral state [13]. Domesticates are not the only exploited species that may act as bioproxies. For example, genetic studies (mitochondrial and nuclear DNA sequences) of the snail Tudorella sulcata indicate that living individuals were moved by people between Sardinia, France, and Algeria [15]. One likely explanation is that the shell of this snail was used as an ornament in the Neolithic period, making it a good bioproxy for Neolithic movements in the Mediterranean.

The term ‘commensal’ has various usages, but here describes a spectrum of species that opportunistically exploit habitats and food sources around humans (particularly dwellings and nearby areas) and are readily transported by humans. Commensals in this sense can vary between having no discernible negative effect on humans to being pests, and the same organism can span this continuum under different circumstances. Interestingly, several commensals are important biological models, most notably the fruit fly [16], rat [17], and mouse (the focus of this article); presumably their commensalism makes them noticeable and available to humans, and likely to fare well in captivity. The progenitors of the laboratory fruit fly and rat, Drosophila melanogaster and Rattus norvegicus, have predominantly been moved around by people in the past 200–300 years 16 and 18, and thus have limited value as bioproxies for human history. However, other commensal rats, including the ship rat, R. rattus (Box 2 19 and 20), and in particular the Pacific rat, R. exulans, have been of more interest in this regard. Although it lives around human dwellings, as expected for a typical commensal, R. exulans, similarly to the pig, may actually have been transported deliberately as food by Polynesians [21]. However, phylogeographic data (mitochondrial DNA) on ancient and modern specimens of the pig and R. exulans provide different perspectives: the former fit the classical model for the colonisation of Oceania by a single spread of the Lapita people [13], and the latter fit a model of multiple introductions and therefore multiple waves of colonisation by people 3 and 22. The value of using multiple bioproxies of various categories to examine a specific problem of human colonisation history is illustrated further in Box 2. As with other types of evidence relating to human history, conflicting results may be obtained, and there is an advantage in having data from a variety of systems.

Of the various possible human associates, pathogens and parasites (as well as other symbionts) are the proxies with the potential to show the closest match in terms of colonisation and demographic histories. This is vividly illustrated by the co-phylogeography of humans and the stomach-living bacterial pathogen Helicobacter pylori, reviewed in [23]. The initial spread of humans out of Africa and the initial colonisation of Europe and the Americas by humans are revealed through multi-locus DNA sequencing of H. pylori. Much more recent events, such as secondary colonisation of the Americas by Europeans and Africans, can also be detected. The bacterial data also reflect human demographic features such as population bottlenecking. The information from genotyping H. pylori appears to be remarkably close to genotyping of humans themselves, and this is explained by the pathogen being readily spread within human families [23], effectively vertical transmission. Pathogens and parasites where transmission is more horizontal are expected to display phylogeographic patterns less closely matched to their human hosts. Nevertheless, there may still be a signal that matches human movements and colonisation history 24 and 25. For instance, the bacterial pathogen that leads to leprosy, Mycobacterium leprae, is one of several pathogens for which the phylogeography can be related to human movements along major trading routes, such as the Silk Road (linking Asia to Europe) and the slave trade (linking West Africa and the Americas) [26]. One limitation of pathogens and parasites is that they are sampled from existing human populations and may not be of use in recovering data about extinct human populations, whereas other bioproxies able to persist independently of humans (e.g., ‘feral’ populations of domesticates or commensals) will still carry a signal.

The house mouse as a model system

The house mouse Mus musculus, the progenitor of the laboratory mouse, is a very familiar commensal living together with, and feeding on the food of, people and their livestock. This close association with humans first began with the M. m. domesticus subspecies around 12 000 years ago in the Near East [27] when mice exploited the niche offered by burgeoning human settlements and grain stores. They have accompanied humans with trade and transport ever since, reaching a near-global distribution [28]. Through this widespread and long-lasting association with humans, mice offer extraordinary possibilities as bioproxies (cats can also be considered in the same co-phylogeographic grouping; Box 3).

Current evidence suggests that M. musculus originated in the north of the Indian subcontinent where it differentiated into three main subspecies, domesticus, musculus, and castaneus, initially through geographic isolation in the Pleistocene 28 and 29; these subspecies independently adopted a commensal human niche. The subsequent range expansion of M. m. domesticus is discussed in more detail below. The M. m. musculus subspecies was spread as a human commensal to northern Eurasia, covering most of the landmass except Western Europe, but including colonisation of Japan 30 and 31. In a comparatively recent human-mediated expansion, M. m. castaneus moved further east and south into southern India, Southeast Asia and Japan, as well as Africa and the Indo-Pacific in historical times [32]. Laboratory mice show varied contributions of these subspecies: the classical inbred strains are overwhelmingly M. m. domesticus but with a genetic contribution of Japanese mice, themselves hybrids of M. m. musculus and M. m. castaneus[33].

House mice are highly adaptable, reproduce rapidly and, in the absence of competitors, can readily establish new populations. It is seemingly rare for an invading female to successfully integrate into an existing population, whereas males can do so [28]. This has made mice ideal proxies to study human history because the signature of the founding females will generally be maintained in maternally inherited mitochondrial DNA, and thus provides an indicator of early human exchanges. Subsequent human trade and migration linked to secondary colonisations of (generally male) mice can be inferred through nuclear (including Y-linked) markers 34 and 35. Large islands, archipelagos, and continental areas may have multiple primary colonisations that can be revealed with mitochondrial DNA, as exemplified by studies on the sub-Antarctic Kerguelen archipelago [36]. Current studies of mitochondrial DNA benefit from a substantial database of D-loop (control region) sequences 32, 37 and 38.

A clear understanding of the phylogeography of house mice, their colonisation history, and the degree to which different lineages (including subspecies) come into secondary contact, underpins other fundamental evolutionary studies in which mice are used as a model, such as those related to speciation, adaptation, and genome evolution 39, 40 and 41.

Western house mice and human history

The phylogeography of the western subspecies of house mouse (M. m. domesticus) provides a case-study for the use of proxies in human history. The subspecies is found in Western Europe, Africa, Australasia, and the Americas, and the observed patterns of mitochondrial D-loop variation provide insights into human movements within and into those areas at various historical periods. Six D-loop clades with subclades within them have been named [42], using similar nomenclature to that in humans. Alternative phylogenetic methods have generated 11 haplogroups [37], many of which can be equated to subdivisions within the six clade scheme [28]. Figure 2 shows the distribution of the six clades over a region from the Near East to the North Atlantic.

Neolithic

The greatest genetic diversity (mitochondrial and X-linked) of the western house mouse occurs in the Near East, consistent with this area being the origin of its commensalism and expansion [28]. Genetic studies on humans have been used to examine human expansion from the Near East [43], including movements into Western Europe during the Neolithic 44 and 45. The mouse expansion into Western Europe occurred much later (in the Iron Age, see below), and mice can therefore only be used as a proxy for Neolithic humans in the Near East region. For example, the colonisation of Anatolia from the Fertile Crescent by house mice during the Neolithic [27] may provide interesting clues in light of current interest in Anatolia for the spread of languages and agriculture further afield [46]. Increasing amounts of D-loop data have been collected for mice in this area, where clades A, B, and C are particularly well-represented (Figure 2) 37 and 47.

Iron Age

Even though house mice occurred around human dwellings during the Neolithic in the Near East, it was not until the Iron Age, about 3000 years ago, that they expanded into Western Europe [27]. The delay may have been caused by the small size of European settlements before the Iron Age, when any house mice that invaded would have been unable to outcompete the native wood mouse, Apodemus sylvaticus; only in larger Iron Age settlements with more commensal habitat could the house mice escape this competition [27]. The increase in maritime transportation during the Iron Age, including Phoenician activities [37], accelerated the sweep of both mice and people through the Mediterranean basin and North Africa. This led to the spread of various mouse D-loop clades across the region 37, 42 and 48; the distribution of clade B is notably representative of this phase (Figure 2). The subsequent expansion of mice northwards [27] is also represented by genetic data, with the penetration of Mediterranean D-loop clades C and D into Central Europe (Figure 2) [42]. Mice may not only reflect Iron Age linkages between the Mediterranean and central Europe, but also between Britain and nearby areas of continental Europe in an area marked by clade E (Figure 2 and Box 4) 42, 49 and 50.

Viking Age

About a thousand years ago, the Norwegian and Danish Vikings had an important presence in the Atlantic periphery of Western Europe. They reached as far as Greenland and Newfoundland in the west and into the Mediterranean basin in the east [51]. The Vikings undoubtedly transported mice [38], and the distributions of clades D and F in particular (Figure 2) appear to have been influenced by Viking dispersal. The value of mice as proxies for Viking history is explored further below and in Box 4.

Age of Discovery

The spread of house mice to coastal Western Europe during the Iron Age and Viking Age enabled a yet further expansion of the species. This area includes the countries that sent out ships that explored and subsequently settled much of the rest of the world from the early 15th century onwards, in other words Portugal, Spain, Britain, France, and The Netherlands. The ships used by the explorers and ensuing settlers would have been infested by mice (and rats), explaining why Captain Cook took cats on his vessels (Box 3) [52]. The mouse genetic data currently available from countries settled by Europeans following the Age of Discovery have a signal that largely matches what is expected from our historical knowledge of the period. For instance, clades E and F, the best-represented clades in the British Isles (Figure 2), are predominant in mice from Australia and New Zealand 49 and 53. However, the mice from the Falkland Islands exhibit a more intriguing pattern. These islands are a British dependency in the South Atlantic, and some of the mice have clade E haplotypes, probably derived from Britain [36]. There are also other mice carrying three D-loop haplotypes (from clade F) identical to those only otherwise found on two islands of the Azores archipelago (S.I. Gabriel et al., unpublished). It is probable that mice were taken from the Azores to the Falklands, and this could have been at the time of discovery rather than at the time of settlement; in the absence of competitors mice can thrive away from human settlements [36]. Mice coming from the Azores may indicate Portuguese discovery, but the Azores could also have been a stopping point for British ships [54]. Although inconclusive in this particular situation, house mice provide evidence of the first discovery of islands and landmasses by the Western European maritime powers, information of value to historians because of the secrecy often associated with such discoveries [55].

In-depth analysis of the co-phylogeography of house mice and Norwegian Vikings

During the Viking period, people from Norway embarked on extensive conquest, colonisation, and settlement of new areas from the late 8th century (Figure 3). Material artefacts reflect these linkages (Figure 1), but human genetics have also been informative. This has shown a general pattern of increasing Norwegian genetic ancestry in the Scottish Western Isles, Orkney, Shetland and Faroe, reaching a maximum in Iceland 56, 57 and 58, where an estimated 64% of the ancestry is Norwegian and 36% Gaelic [57]. A remarkably similar colonisation pattern is seen in the distribution of house mouse mitochondrial DNA, where clade F is restricted almost exclusively to areas under Norwegian Viking influence (Figure 2 and Figure 3) 38, 42 and 50. Using ancient DNA from Viking Age house mouse bones, this clade (indeed, the same haplotype) was also found from the early colonisation period in Iceland continuously to the present day [38]. Mouse samples from the Viking period in Greenland (which lasted until the mid to late 15th century, when the human settlements were abandoned) all belonged to a haplotype one mutation distinct from the common Icelandic haplotype. Like the Vikings themselves, the old Greenlandic strain apparently died out and modern mice sampled in Greenland reflect the recent Danish settlement there (clade D). No trace of clade F was found in modern Newfoundland mice (no ancient samples were available), such that the very short-lived Norwegian Viking colony there (in the early 11th century) left no detectable genetic signature in the mice; again the mice reflect recent human colonisation (probably from southern Britain: clade E). The human patterns of successful colonisation (Iceland) or colonisation and subsequent failure (Greenland, Newfoundland) are mirrored in house mice.

Here, we see a very clear co-phylogeographic pattern of house mice and humans (of European descent), and the indisputable potential of house mice as bioproxies for Norwegian Viking history. However, the situation is not completely clear-cut. Norway itself is occupied by a mix of different mouse clades (Figure 3), potentially explained as the simultaneous multiple arrivals of mice from various areas via maritime routes, reflecting the sudden explosion of seafaring expeditions from Norway during the Viking period [51]. The Faroe Islands are occupied by clade D which may have arrived from southern rather than northern Norway (Figure 3) [59], consistent with what is known historically about the human colonisation of the islands [60].

Future directions

Overwhelmingly, phylogeographic studies on the western house mouse have been conducted with a single mitochondrial marker, the D-loop. However, greater precision can be obtained from genomic approaches. Given that maternally inherited markers may be particularly valuable to yield information on first colonisation of an area, complete mitochondrial genomes are an obvious and relatively easy first step [61]. However, the house mouse as a model will not properly be exploited until use is made of tools to investigate the nuclear genome, such as the 623 124 SNP Mouse Diversity Array [62]. These will allow analysis of multiple colonisations of a particular area, and there are also likely to be interesting patterns involving selection and adaptive introgression [40]. Genomic data of this sort are amenable to demographic modelling, including the Approximate Bayesian Computation approach [63]. Figure 4 shows an example of a hypothetical population history of house mouse populations involved in colonisation events. With sufficient depth and quantity of genomic data, it would be possible to reveal scenarios such as this with demographic modelling. Because much of the house mouse history is in synchrony with human populations, if genetic analysis can determine demographic changes of this type in mouse populations over time, the mouse can be a particularly valuable proxy. What is true for the house mouse can also be applied to other bioproxies, and for any of these types of study there is a substantial benefit to include specimens contemporary to the actual events being modelled (via ancient DNA). In this way the full power of genomes and genetics can make a substantial difference in historical inference. Such studies will not replace evidence from material artefacts and documentary sources, but they have the potential to have a very large impact on our understanding of history.

Concluding remarks

Studying humans is the most direct route to understanding ourselves, and just as biomedical studies on mice and other species can help us understand human physiology and genetics, so studies on bioproxies can contribute substantially to our understanding of human colonisation and demographic history. Many organisms can potentially be used as bioproxies (e.g., domesticates, commensals, pathogens, and parasites) and, by combining these in a co-phylogeographic framework with human data, we can use them to study human populations during particular periods of historical interest. House mice have lived with and been moved around by people for ∼12 000 years, and there are many instances where studies on their colonisation history are linked with human phylogeographic studies, such as the Neolithic expansion through Europe [43], the Phoenician spread through the Mediterranean [64], and the Viking colonisation of North Atlantic islands 56, 57 and 58. So far, studies on house mice have largely used mitochondrial D-loop sequences. In the future, applying the combination of genomic methods and demographic modelling to house mice will allow much more precise understanding of particular historical events and the complexity of repeated human (and therefore murine) colonisations into one geographical area. Typically treated as vermin, house mice could rather be considered as genetic historical treasures that are, in our collective experience, a numerically fast-declining part of our cultural heritage in many countries (in Western Europe at least).

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