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Wang X, Heckel G. Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles. Genome Res 2024; 34:851-862. [PMID: 38955466 PMCID: PMC11293545 DOI: 10.1101/gr.278487.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 05/14/2024] [Indexed: 07/04/2024]
Abstract
Island populations often experience different ecological and demographic conditions than their counterparts on the continent, resulting in divergent evolutionary forces affecting their genomes. Random genetic drift and selection both may leave their imprints on island populations, although the relative impact depends strongly on the specific conditions. Here we address their contributions to the island syndrome in a rodent with an unusually clear history of isolation. Common voles (Microtus arvalis) were introduced by humans on the Orkney archipelago north of Scotland >5000 years ago and rapidly evolved to exceptionally large size. Our analyses show that the genomes of Orkney voles were dominated by genetic drift, with extremely low diversity, variable Tajima's D, and very high divergence from continental conspecifics. Increased d N/d S ratios over a wide range of genes in Orkney voles indicated genome-wide relaxation of purifying selection. We found evidence of hard sweeps on key genes of the lipid metabolism pathway only in continental voles. The marked increase of body size in Orkney-a typical phenomenon of the island syndrome-may thus be associated to the relaxation of positive selection on genes related to this pathway. On the other hand, a hard sweep on immune genes of Orkney voles likely reflects the divergent ecological conditions and possibly the history of human introduction. The long-term isolated Orkney voles show that adaptive changes may still impact the evolutionary trajectories of such populations despite the pervasive consequences of genetic drift at the genome level.
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Affiliation(s)
- Xuejing Wang
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland;
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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Wang X, Peischl S, Heckel G. Demographic history and genomic consequences of 10,000 generations of isolation in a wild mammal. Curr Biol 2023; 33:2051-2062.e4. [PMID: 37178689 DOI: 10.1016/j.cub.2023.04.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/20/2022] [Accepted: 04/17/2023] [Indexed: 05/15/2023]
Abstract
Increased human activities caused the isolation of populations in many species-often associated with genetic depletion and negative fitness effects. The effects of isolation are predicted by theory, but long-term data from natural populations are scarce. We show, with full genome sequences, that common voles (Microtus arvalis) in the Orkney archipelago have remained genetically isolated from conspecifics in continental Europe since their introduction by humans over 5,000 years ago. Modern Orkney vole populations are genetically highly differentiated from continental conspecifics as a result of genetic drift processes. Colonization likely started on the biggest Orkney island and vole populations on smaller islands were gradually split off, without signs of secondary admixture. Despite having large modern population sizes, Orkney voles are genetically depauperate and successive introductions to smaller islands resulted in further reduction of genetic diversity. We detected high levels of fixation of predicted deleterious variation compared with continental populations, particularly on smaller islands, yet the fitness effects realized in nature are unknown. Simulations showed that predominantly mildly deleterious mutations were fixed in populations, while highly deleterious mutations were purged early in the history of the Orkney population. Relaxation of selection overall due to benign environmental conditions on the islands and the effects of soft selection may have contributed to the repeated, successful establishment of Orkney voles despite potential fitness loss. Furthermore, the specific life history of these small mammals, resulting in relatively large population sizes, has probably been important for their long-term persistence in full isolation.
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Affiliation(s)
- Xuejing Wang
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Stephan Peischl
- Interfaculty Bioinformatics Unit, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland; Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland; Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland.
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Romaniuk AA, Troalen LG, Bendrey R, Herman JS, Owen O, Smith C. Pests or prey? Micromammal species within an ancient anthropic environment at the Norse settlement site of Tuquoy (Westray, Orkney). ROYAL SOCIETY OPEN SCIENCE 2023; 10:221462. [PMID: 37035288 PMCID: PMC10073909 DOI: 10.1098/rsos.221462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
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.
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Affiliation(s)
- Andrzej A. Romaniuk
- School of History, Classics and Archaeology, The University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
- Institute for Advanced Studies in the Humanities, The University of Edinburgh, Hope Park Square, Edinburgh EH8 9NW, UK
| | - Lore G. Troalen
- Department of Collections Services, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
| | - Robin Bendrey
- School of History, Classics and Archaeology, The University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Jeremy S. Herman
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
| | - Olwyn Owen
- Institute of Archaeology, University of the Highlands and Islands, Orkney College, East Road, Kirkwall, Orkney KW15 1LX
| | - Catherine Smith
- Alder Archaeology Ltd, 55 South Methven Street, Perth PH1 5NX, UK
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Häberle S, Schäfer M, Soteras R, Martínez-Grau H, Hajdas I, Jacomet S, Röder B, Schibler J, van Willigen S, Antolín F. 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). Animals (Basel) 2022; 12:1511. [PMID: 35739848 PMCID: PMC9219518 DOI: 10.3390/ani12121511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/31/2022] [Accepted: 06/04/2022] [Indexed: 11/16/2022] Open
Abstract
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.
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Affiliation(s)
- Simone Häberle
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science (IPAS), Basel University, 4055 Basel, Switzerland; (R.S.); (H.M.-G.); (S.J.); (J.S.); (F.A.)
| | - Marguerita Schäfer
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science (IPAS), Basel University, 4055 Basel, Switzerland; (R.S.); (H.M.-G.); (S.J.); (J.S.); (F.A.)
| | - Raül Soteras
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science (IPAS), Basel University, 4055 Basel, Switzerland; (R.S.); (H.M.-G.); (S.J.); (J.S.); (F.A.)
- Deutsches Archäologisches Institut, Referat Naturwissenschaften an der Zentrale, 14195 Berlin, Germany
| | - Héctor Martínez-Grau
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science (IPAS), Basel University, 4055 Basel, Switzerland; (R.S.); (H.M.-G.); (S.J.); (J.S.); (F.A.)
| | - Irka Hajdas
- Laboratory of Ion Beam Physics (LIP), Swiss Federal Institute of Technology (ETH) Zurich, 8093 Zurich, Switzerland;
| | - Stefanie Jacomet
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science (IPAS), Basel University, 4055 Basel, Switzerland; (R.S.); (H.M.-G.); (S.J.); (J.S.); (F.A.)
| | - Brigitte Röder
- Departement Altertumswissenschaften, Ur- und Frühgeschichtliche und Provinzialrömische Archäologie, Basel University, 4051 Basel, Switzerland;
| | - Jörg Schibler
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science (IPAS), Basel University, 4055 Basel, Switzerland; (R.S.); (H.M.-G.); (S.J.); (J.S.); (F.A.)
| | | | - Ferran Antolín
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science (IPAS), Basel University, 4055 Basel, Switzerland; (R.S.); (H.M.-G.); (S.J.); (J.S.); (F.A.)
- Deutsches Archäologisches Institut, Referat Naturwissenschaften an der Zentrale, 14195 Berlin, Germany
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Chevret P, Hautier L, Ganem G, Herman J, Agret S, Auffray JC, Renaud S. Genetic structure in Orkney island mice: isolation promotes morphological diversification. Heredity (Edinb) 2020; 126:266-278. [PMID: 32980864 DOI: 10.1038/s41437-020-00368-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/04/2020] [Accepted: 09/04/2020] [Indexed: 11/09/2022] Open
Abstract
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.
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Affiliation(s)
- Pascale Chevret
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558 CNRS Université Lyon 1, Université de Lyon, Campus de la Doua, 69100, Villeurbanne, France.
| | - Lionel Hautier
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Guila Ganem
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Jeremy Herman
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh, EH1 1JF, UK
| | - Sylvie Agret
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Jean-Christophe Auffray
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Sabrina Renaud
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558 CNRS Université Lyon 1, Université de Lyon, Campus de la Doua, 69100, Villeurbanne, France
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Puckett EE, Orton D, Munshi‐South J. Commensal Rats and Humans: Integrating Rodent Phylogeography and Zooarchaeology to Highlight Connections between Human Societies. Bioessays 2020; 42:e1900160. [DOI: 10.1002/bies.201900160] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/09/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Emily E. Puckett
- Department of Biological SciencesUniversity of Memphis Memphis TN 38152 USA
| | - David Orton
- BioArChDepartment of ArchaeologyUniversity of York York YO10 5DD UK
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Erdal O, Sen S, Erturaç MK, Bıçakçı E. The rodent fauna from the Neolithic human settlement of Tepecik-Çiftlik (Niğde, Turkey). MAMMALIA 2018. [DOI: 10.1515/mammalia-2018-0006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The primary aim of this study was to establish for the very first time the results on the rodent fauna gathered from the ongoing Neolithic excavations at the Tepecik-Çiftlik site in southern Cappadocia (Niğde, Turkey). So far, the fauna being study is represented by species of arvicolines (Microtus cf. arvalis and Arvicola cf. amphibius), murines (Mus cf. musculus), sousliks (Spermophilus xanthoprymnus), hamsters (Mesocricetus brandti) and mole-rats (Spalax xanthodon), and their remains are described in detail. Paleoenvironmental assumption based on common preferences of the fauna elements indicates, at first sight, a rather dry steppe environment with sparse plant cover or perennial short grasses. On the other hand, the presence of Arvicola cf. amphibius points out streams and marsh-like vegetation cover with bodies of water . The predation or burn marks observed on some specimens and the presence of subterraneous rodents raise questions concerning their taphonomy.
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Affiliation(s)
- Ozan Erdal
- Eurasia Institute of Earth Sciences, Istanbul Technical University , 34469, Maslak , Istanbul , Turkey
| | - Sevket Sen
- Muséum National d’Histoire Naturelle , 8, rue Buffon , Paris 75005 , France
| | - M. Korhan Erturaç
- Department of Geography , Sakarya University , Sakarya 54187 , Turkey
| | - Erhan Bıçakçı
- Prehistory Section , Istanbul University , 34459 Laleli , Istanbul , Turkey
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