1
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Li J, Huang E, Wu Y, Zhu C, Li W, Ai L, Xie Q, Tian Z, Zhong W, Sun G, Zhang L, Tan W. Population structure, dispersion patterns and genetic diversity of two major invasive and commensal zoonotic disease hosts ( Rattus norvegicus and Rattus tanezumi) from the southeastern coast of China. Front Genet 2024; 14:1174584. [PMID: 38259625 PMCID: PMC10800861 DOI: 10.3389/fgene.2023.1174584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
Background: The invasive brownrat (Rattus norvegicus) and the Oriental rats (Rattus tanezumi) are common commensal murid that are important hosts for rodent-borne diseases in southeast Asia. Understanding their population structure and genetic diversity is essential to uncover their invasion biology and distribution dynamics that are essential for controlling rodent-borne diseases. Methods: TA total of 103 R. norvegicus and 85 R. tanezumi were collected from 13 to 9 coastal areas of six provincial monitoring sentinel sites, respectivelyto assess patterns in their microsatellite loci and their mitochondrial coxl gene region. Results: Eleven sampled populations of R. norvegicus were divided into two major clusters by region. The observed heterozygosity values of all regional populations were smaller than expected genetic diversity heterozygosity values and deviated from Hardy-Weinberg equilibrium Nine sample populations of R. tanezumi were divided into three clusters; two that included sample from Hainan and Fujian provinces, and one that included samples from the other provinces and cities. The genetic diversity of R. tanezumi was highest in samples from Jiangsu and Guangdong provinces. Conclusion: The data in this paper confirm the two invasive rodent species from the southeastern coastal region of China may have relied on maritime transport to spread from the southern region of China to the Yangtze River basin. R. tanezumi may then hanve migrated unidirectionally, along the southeastern provinces of China towards the north, while R. norvegicus spread in a complex and multidirectional manner in Hainan, Fujian, Zhejiang and Jiangsu Provinces of the country.
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Affiliation(s)
- Jiaqiao Li
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
- School of Resources and Chemical Engineering, Sanming University, Sanming, China
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Enjiong Huang
- Technology Center of Fuzhou Customs, Fuzhou, Fujian, China
| | - Yifan Wu
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Changqiang Zhu
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Wenhao Li
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Lele Ai
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Qinghua Xie
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhi Tian
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
| | - Weiwen Zhong
- Center for Disease Control and Prevention, Longquan, Zhejiang, China
| | - Gang Sun
- School of Resources and Chemical Engineering, Sanming University, Sanming, China
| | - Lingling Zhang
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weilong Tan
- Nanjing Bioengineering (Gene) Technology Center for Medicines, Nanjing, China
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2
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Implications of anomalous relative sea-level rise for the peopling of Remote Oceania. Proc Natl Acad Sci U S A 2022; 119:e2210863119. [PMID: 36534809 PMCID: PMC9907147 DOI: 10.1073/pnas.2210863119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Beginning ~3,500 to 3,300 y B.P., humans voyaged into Remote Oceania. Radiocarbon-dated archaeological evidence coupled with cultural, linguistic, and genetic traits indicates two primary migration routes: a Southern Hemisphere and a Northern Hemisphere route. These routes are separated by low-lying, equatorial atolls that were settled during secondary migrations ~1,000 y later after their exposure by relative sea-level fall from a mid-Holocene highstand. High volcanic islands in the Federated States of Micronesia (Pohnpei and Kosrae) also lie between the migration routes and settlement is thought to have occurred during the secondary migrations despite having been above sea level during the initial settlement of Remote Oceania. We reconstruct relative sea level on Pohnpei and Kosrae using radiocarbon-dated mangrove sediment and show that, rather than falling, there was a ~4.3-m rise over the past ~5,700 y. This rise, likely driven by subsidence, implies that evidence for early settlement could lie undiscovered below present sea level. The potential for earlier settlement invites reinterpretation of migration pathways into Remote Oceania and monument building. The UNESCO World Heritage sites of Nan Madol (Pohnpei) and Leluh (Kosrae) were constructed when relative sea level was ~0.94 m (~770 to 750 y B.P.) and ~0.77 m (~640 to 560 y B.P.) lower than present, respectively. Therefore, it is unlikely that they were originally constructed as islets separated by canals filled with ocean water, which is their prevailing interpretation. Due to subsidence, we propose that these islands and monuments are more vulnerable to future relative sea-level rise than previously identified.
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3
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Escoriza D. Success factors of great oceanic dispersers: Case of Squamata in the Pacific Ocean. J Zool (1987) 2022. [DOI: 10.1111/jzo.13042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- D. Escoriza
- GRECO, Institute of Aquatic Ecology University of Girona, Campus de Montillivi Girona Spain
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4
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Jing M, Chen Y, Yao K, Wang Y, Huang L. Comparative phylogeography of two commensal rat species ( Rattus tanezumi and Rattus norvegicus) in China: Insights from mitochondrial DNA, microsatellite, and 2b-RAD data. Ecol Evol 2022; 12:e9409. [PMID: 36254297 PMCID: PMC9557235 DOI: 10.1002/ece3.9409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/09/2022] [Accepted: 09/20/2022] [Indexed: 11/10/2022] Open
Abstract
Rattus norvegicus and Rattus tanezumi are dominant species of Chinese house rats, but the colonization and demographic history of two species in China have not been thoroughly explored. Phylogenetic analyses with mitochondrial DNA including 486 individuals from 31 localities revealed that R. norvegicus is widely distributed in China, R. tanezumi is mainly distributed in southern China with currently invading northward; northeast China was the natal region of R. norvegicus, while the spread of R. tanezumi in China most likely started from the southeast coast. A total of 123 individuals from 18 localities were subjected to 2b-RAD analyses. In neighbor-joining tree, individuals of R. tanezumi grouped into geographic-specific branches, and populations from southeast coast were ancestral groups, which confirmed the colonization route from southeast coast to central and western China. However, individuals of R. norvegicus were generally grouped into two clusters instead of geographic-specific branches. One cluster comprised inland populations, and another cluster included both southeast coast and inland populations, which indicated that spread history of R. norvegicus in China was complex; in addition to on-land colonization, shipping transportation also have played great roles. ADMIXTURE and principal component analyses provided further supports for the colonization history. Demographic analyses revealed that climate changes at ~40,000 to 18,000 years ago and ~4000 years ago had led to population declines of both species; the R. norvegicus declined rapidly while the population of R. tanezumi continuously expanded since ~1500 years ago, indicating the importance of interspecies' competition in their population size changes. Our study provided a valuable framework for further investigation on phylogeography of two species in China.
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Affiliation(s)
- Meidong Jing
- School of Life SciencesNantong UniversityNantongChina
| | - Yingjie Chen
- School of Life SciencesNantong UniversityNantongChina
| | - Keying Yao
- School of Life SciencesNantong UniversityNantongChina
| | - Youming Wang
- School of Life SciencesNantong UniversityNantongChina
| | - Ling Huang
- School of Life SciencesNantong UniversityNantongChina
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5
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Amis Pacilo and Yami Cipoho are not the same as the Pacific breadfruit starch crop—Target enrichment phylogenomics of a long-misidentified Artocarpus species sheds light on the northward Austronesian migration from the Philippines to Taiwan. PLoS One 2022; 17:e0272680. [PMID: 36178903 PMCID: PMC9524695 DOI: 10.1371/journal.pone.0272680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/10/2022] [Indexed: 11/23/2022] Open
Abstract
‘Breadfruit’ is a common tree species in Taiwan. In the indigenous Austronesian Amis culture of eastern Taiwan, ‘breadfruit’ is known as Pacilo, and its fruits are consumed as food. On Lanyu (Botel Tobago) where the indigenous Yami people live, ‘breadfruit’ is called Cipoho and used for constructing houses and plank-boats. Elsewhere in Taiwan, ‘breadfruit’ is also a common ornamental tree. As an essential component of traditional Yami culture, Cipoho has long been assumed to have been transported from the Batanes Island of the Philippines to Lanyu. As such, it represents a commensal species that potentially can be used to test the hypothesis of the northward Austronesian migration ‘into’ Taiwan. However, recent phylogenomic studies using target enrichment show that Taiwanese ‘breadfruit’ might not be the same as the Pacific breadfruit (Artocarpus altilis), which was domesticated in Oceania and widely cultivated throughout the tropics. To resolve persistent misidentification of this culturally and economically important tree species of Taiwan, we sampled 36 trees of Taiwanese Artocarpus and used the Moraceae probe set to enrich 529 nuclear genes. Along with 28 archived Artocarpus sequence datasets (representing a dozen taxa from all subgenera), phylogenomic analyses showed that all Taiwanese ‘breadfruit’ samples, together with a cultivated ornamental tree from Hawaii, form a fully supported clade within the A. treculianus complex, which is composed only of endemic Philippine species. Morphologically, the Taiwanese ‘breadfruit’ matches the characters of A. treculianus. Within the Taiwanese samples of A. treculianus, Amis samples form a fully supported clade derived from within the paraphyletic grade composed of Yami samples, suggesting a Lanyu origin. Results of our target enrichment phylogenomics are consistent with the scenario that Cipoho was transported northward from the Philippines to Lanyu by Yami ancestors, though the possibility that A. treculianus is native to Lanyu cannot be ruled out completely.
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6
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Shaw B, Hawkins S, Becerra-Valdivia L, Turney CSM, Coxe S, Kewibu V, Haro J, Miamba K, Leclerc M, Spriggs M, Privat K, Haberle S, Hopf F, Hull E, Pengilley A, Brown S, Marjo CE, Jacobsen G. Frontier Lapita interaction with resident Papuan populations set the stage for initial peopling of the Pacific. Nat Ecol Evol 2022; 6:802-812. [PMID: 35449459 DOI: 10.1038/s41559-022-01735-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 03/10/2022] [Indexed: 11/09/2022]
Abstract
The initial peopling of the remote Pacific islands was one of the greatest migrations in human history, beginning three millennia ago by Lapita cultural groups. The spread of Lapita out of an ancestral Asian homeland is a dominant narrative in the origins of Pacific peoples, and although Island New Guinea has long been recognized as a springboard for the peopling of Oceania, the role of Indigenous populations in this remarkable phase of exploration remains largely untested. Here, we report the earliest evidence for Lapita-introduced animals, turtle bone technology and repeated obsidian import in southern New Guinea 3,480-3,060 years ago, synchronous with the establishment of the earliest known Lapita settlements 700 km away. Our findings precede sustained Lapita migrations and pottery introductions by several centuries, occur alongside Indigenous technologies and suggest continued multicultural influences on population diversity despite language replacement. Our work shows that initial Lapita expansion throughout Island New Guinea was more expansive than previously considered, with Indigenous contact influencing migration pathways and island-hopping strategies that culminated in rapid and purposeful Pacific-wide settlement. Later Lapita dispersals through New Guinea were facilitated by earlier contact with Indigenous populations and profoundly influenced the region as a global centre of cultural and linguistic diversity.
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Affiliation(s)
- Ben Shaw
- Evolution of Cultural Diversity Initiative, School of Culture, History and Language, College of Asia and the Pacific, The Australian National University, Canberra, Australian Capital Territory, Australia. .,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia. .,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, School of Culture, History and Language, Australian National University, Canberra, Australian Capital Territory, Australia. .,Australian Research Council Centre of Excellence for the Dynamics of Language, School of Culture, History and Language, Australian National University, Canberra, Australian Capital Territory, Australia. .,School of Culture, History and Language, College of Asia and the Pacific, The Australian National University, Canberra, Australian Capital Territory, Australia.
| | - Stuart Hawkins
- School of Culture, History and Language, College of Asia and the Pacific, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Lorena Becerra-Valdivia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.,Chronos 14Carbon Cycle Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia.,Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, School of Archaeology, University of Oxford, Oxford, UK
| | - Chris S M Turney
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.,Chronos 14Carbon Cycle Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia.,Division of the Deputy Vice-Chancellor (Research), University of Technology Sydney, Sydney, New South Wales, Australia
| | - Simon Coxe
- Evolution of Cultural Diversity Initiative, School of Culture, History and Language, College of Asia and the Pacific, The Australian National University, Canberra, Australian Capital Territory, Australia.,Monash Indigenous Studies Centre, Monash University, Melbourne, Victoria, Australia
| | - Vincent Kewibu
- School of Humanities and Social Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - Jemina Haro
- National Museum and Art Gallery of Papua New Guinea, Port Moresby, Papua New Guinea
| | - Kenneth Miamba
- National Museum and Art Gallery of Papua New Guinea, Port Moresby, Papua New Guinea
| | - Mathieu Leclerc
- School of Culture, History and Language, College of Asia and the Pacific, The Australian National University, Canberra, Australian Capital Territory, Australia.,School of Archaeology and Anthropology, College of Arts and Social Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Matthew Spriggs
- School of Archaeology and Anthropology, College of Arts and Social Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia.,Vanuatu Cultural Centre, Port Vila, Vanuatu
| | - Karen Privat
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.,Electron Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Simon Haberle
- Evolution of Cultural Diversity Initiative, School of Culture, History and Language, College of Asia and the Pacific, The Australian National University, Canberra, Australian Capital Territory, Australia.,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, School of Culture, History and Language, Australian National University, Canberra, Australian Capital Territory, Australia.,School of Culture, History and Language, College of Asia and the Pacific, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Felicitas Hopf
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, School of Culture, History and Language, Australian National University, Canberra, Australian Capital Territory, Australia.,School of Culture, History and Language, College of Asia and the Pacific, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Emily Hull
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Alana Pengilley
- Faculty of Arts and Social Sciences, The University of Sydney, Sydney, New South Wales, Australia.,Department of Anthropology, College of Liberal Arts, University of Texas, Austin, TX, USA
| | - Samantha Brown
- Institute for Scientific Archaeology, Eberhard Karls University of Tübingen, Tubingen, Germany
| | - Christopher E Marjo
- Chronos 14Carbon Cycle Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Geraldine Jacobsen
- Centre for Accelerator Science, Australian Nuclear Science and Technology Organisation, Lucas Heights, Sydney, New South Wales, Australia
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7
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Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history. Nat Commun 2022; 13:2399. [PMID: 35504912 PMCID: PMC9064997 DOI: 10.1038/s41467-022-30009-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 03/18/2022] [Indexed: 11/29/2022] Open
Abstract
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.’
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8
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Wohlwend MR, Craven D, Weigelt P, Seebens H, Winter M, Kreft H, Dawson W, Essl F, van Kleunen M, Pergl J, Pyšek P, Space J, Thomas P, Knight T. Data Descriptor: Pacific Introduced Flora (PaciFLora). Biodivers Data J 2021; 9:e67318. [PMID: 34385884 PMCID: PMC8316249 DOI: 10.3897/bdj.9.e67318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/14/2021] [Indexed: 11/12/2022] Open
Abstract
Background The Pacific Region has the highest density of naturalised plant species worldwide, which makes it an important area for research on the ecology, evolution and biogeography of biological invasions. While different data sources on naturalised plant species exist for the Pacific, there is no taxonomically and spatially harmonised database available for different subsets of species and islands. A comprehensive, accessible database containing the distribution of naturalised vascular plant species in the Pacific will enable new basic and applied research for researchers and will be an important information source for practitioners working in the Region. New information Here, we present PacIFlora, an updated and taxonomically standardised list of naturalised species, their unified nativeness, cultivation and invasive status and their distribution across the Pacific Ocean, including harmonised location denoination. This list is based on the two largest databases on naturalised plants for the Region, specifically the Pacific Island Ecosystems at Risk (PIER) and the Global Naturalised Alien Flora (GloNAF) databases. We provide an outlook for how this database can contribute to numerous research questions and conservation efforts.
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Affiliation(s)
- Michael Rudolf Wohlwend
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany Institute of Biology, Martin Luther University Halle-Wittenberg Halle (Saale) Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany
| | - Dylan Craven
- Universidad Mayor, Santiago, Chile Universidad Mayor Santiago Chile
| | - Patrick Weigelt
- Department of Biodiversity, Macroecology & Biogeography, Faculty of Forest Sciences, University of Göttingen, Göttingen, Germany Department of Biodiversity, Macroecology & Biogeography, Faculty of Forest Sciences, University of Göttingen Göttingen Germany
| | - Hanno Seebens
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany Senckenberg Biodiversity and Climate Research Centre (SBiK-F) Frankfurt am Main Germany
| | - Marten Winter
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany
| | - Holger Kreft
- Department of Biodiversity, Macroecology & Biogeography, Faculty of Forest Sciences, University of Göttingen, Göttingen, Germany Department of Biodiversity, Macroecology & Biogeography, Faculty of Forest Sciences, University of Göttingen Göttingen Germany
| | - Wayne Dawson
- Durham University, Durham, United Kingdom Durham University Durham United Kingdom
| | - Franz Essl
- BioInvasions, Global Change, Macroecology-Group, Department of Botany and Biodiversity Research, University Vienna, Vienna, Austria BioInvasions, Global Change, Macroecology-Group, Department of Botany and Biodiversity Research, University Vienna Vienna Austria.,Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University Stellenbosch South Africa
| | - Mark van Kleunen
- University of Konstanz, Konstanz, Germany University of Konstanz Konstanz Germany
| | - Jan Pergl
- Czech Academy of Sciences, Institute of Botany, Department of Invasion Ecology, Průhonice, Czech Republic Czech Academy of Sciences, Institute of Botany, Department of Invasion Ecology Průhonice Czech Republic
| | - Petr Pyšek
- Institute of Botany, Průhonice, Czech Republic Institute of Botany Průhonice Czech Republic.,Academy of Sciences of the Czech Republic, Pruhonice, Czech Republic Academy of Sciences of the Czech Republic Pruhonice Czech Republic
| | - James Space
- Pacific Southwest Research Station, USDA Forest Service (ret.), Sun Lakes, United States of America Pacific Southwest Research Station, USDA Forest Service (ret.) Sun Lakes United States of America
| | - Philip Thomas
- Hawaiian Ecosystems at Risk project, Carrboro, United States of America Hawaiian Ecosystems at Risk project Carrboro United States of America
| | - Tiffany Knight
- Martin-Luther-Universität Halle-Wittenberg, Leipzig, Germany Martin-Luther-Universität Halle-Wittenberg Leipzig Germany
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9
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The first quantitative assessment of radiocarbon chronologies for initial pottery in Island Southeast Asia supports multi-directional Neolithic dispersal. PLoS One 2021; 16:e0251407. [PMID: 34077445 PMCID: PMC8171956 DOI: 10.1371/journal.pone.0251407] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 04/27/2021] [Indexed: 11/29/2022] Open
Abstract
Neolithization, or the Holocene demographic expansion of farming populations, accounts for significant changes in human and animal biology, artifacts, languages, and cultures across the earth. For Island Southeast Asia, the orthodox Out of Taiwan hypothesis proposes that Neolithic expansion originated from Taiwan with populations moving south into Island Southeast Asia, while the Western Route Migration hypothesis suggests the earliest farming populations entered from Mainland Southeast Asia in the west. These hypotheses are also linked to competing explanations of the Austronesian expansion, one of the most significant population dispersals in the ancient world that influenced human and environmental diversity from Madagascar to Easter Island and Hawai‘i to New Zealand. The fundamental archaeological test of the Out of Taiwan and Western Route Migration hypotheses is the geographic and chronological distribution of initial pottery assemblages, but these data have never been quantitatively analyzed. Using radiocarbon determinations from 20 archaeological sites, we present a Bayesian chronological analysis of initial pottery deposition in Island Southeast Asia and western Near Oceania. Both site-scale and island-scale Bayesian models were produced in Oxcal using radiocarbon determinations that are most confidently associated with selected target events. Our results indicate multi-directional Neolithic dispersal in Island Southeast Asia, with the earliest pottery contemporaneously deposited in western Borneo and the northern Philippines. This work supports emerging research that identifies separate processes of biological, linguistic, and material culture change in Island Southeast Asia.
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10
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da Silva Coelho FA, Gill S, Tomlin CM, Heaton TH, Lindqvist C. An early dog from southeast Alaska supports a coastal route for the first dog migration into the Americas. Proc Biol Sci 2021; 288:20203103. [PMID: 33622130 PMCID: PMC7934960 DOI: 10.1098/rspb.2020.3103] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The oldest confirmed remains of domestic dogs in North America are from mid-continent archaeological sites dated approximately 9900 calibrated years before present (cal BP). Although this date suggests that dogs may not have arrived alongside the first Native Americans, the timing and routes for the entrance of New World dogs remain uncertain. Here, we present a complete mitochondrial genome of a dog from southeast Alaska, dated to 10 150 ± 260 cal BP. We compared this high-coverage genome with data from modern dog breeds, historical Arctic dogs and American precontact dogs (PCDs) from before European arrival. Our analyses demonstrate that the ancient dog belongs to the PCD lineage, which diverged from Siberian dogs around 16 700 years ago. This timing roughly coincides with the minimum suggested date for the opening of the North Pacific coastal (NPC) route along the Cordilleran Ice Sheet and genetic evidence for the initial peopling of the Americas. This ancient southeast Alaskan dog occupies an early branching position within the PCD clade, indicating it represents a close relative of the earliest PCDs that were brought alongside people migrating from eastern Beringia southward along the NPC to the rest of the Americas. The stable isotope δ13C value of this early dog indicates a marine diet, different from the younger mid-continent PCDs' terrestrial diet. Although PCDs were largely replaced by modern European dog breeds, our results indicate that their population decline started approximately 2000 years BP, coinciding with the expansion of Inuit peoples, who are associated with traditional sled-dog culture. Our findings suggest that dogs formed part of the initial human habitation of the New World, and provide insights into their replacement by both Arctic and European lineages.
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Affiliation(s)
| | - Stephanie Gill
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Crystal M Tomlin
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Timothy H Heaton
- Department of Earth Sciences, University of South Dakota, Vermillion, SD 57069, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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11
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Elliott TF, Vernes K. Notes on the diets of four rodent species from Goodenough Island. AUSTRALIAN MAMMALOGY 2021. [DOI: 10.1071/am20022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Goodenough Island is in the Milne Bay Province of Papua New Guinea and is located off of New Guinea’s eastern coast. Goodenough Island has a unique yet poorly studied mammal community. Previous dietary study of mycophagous New Guinean forest wallabies showed that Goodenough Island’s endemic black forest wallaby (Dorcopsis atrata) ate at least 12 taxa of fungi. Using spirit collections at the Australian Museum in Sydney, we evaluated and compared fungal diversity in rodent diets on the same island. We sampled diets of four Goodenough Island rodent species (Chiruromys forbesi, Paramelomys platyops, Rattus exulans and Rattus mordax) and show that fungi are dietary components for three of these mammals.
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12
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Miller‐ter Kuile A, Orr D, Bui A, Dirzo R, Klope M, McCauley D, Motta C, Young H. Impacts of rodent eradication on seed predation and plant community biomass on a tropical atoll. Biotropica 2020. [DOI: 10.1111/btp.12864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ana Miller‐ter Kuile
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara CA USA
| | - Devyn Orr
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara CA USA
| | - An Bui
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara CA USA
| | - Rodolfo Dirzo
- Department of Biology Stanford University Stanford CA USA
| | - Maggie Klope
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara CA USA
| | - Douglas McCauley
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara CA USA
| | - Carina Motta
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara CA USA
| | - Hillary Young
- Department of Ecology, Evolution, and Marine Biology University of California, Santa Barbara Santa Barbara CA USA
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13
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Late Quaternary Environmental and Human Impacts on the Mitochondrial DNA Diversity of Four Commensal Rodents in Myanmar. J MAMM EVOL 2020. [DOI: 10.1007/s10914-020-09519-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AbstractWe addressed the spatiotemporal characteristics of four commensal rodent species occurring in Myanmar in comparison with other areas of the Indo-Malayan region. We examined sequence variations of the mitochondrial cytochrome b gene (Cytb) in the Pacific rat (Rattus exulans), roof rat (Rattus rattus complex, RrC), lesser bandicoot rat (Bandicota bengalensis), and house mouse (Mus musculus) using the recently developed time-dependent evolutionary rates of mtDNA. The Cytb sequences of RrC from Myanmar were shown to belong to RrC Lineage II, and their level of genetic diversity was relatively high compared to those of the other three species. RrC was found to have experienced bottleneck and rapid expansion events at least twice in the late Pleistocene period in Myanmar and a nearby region. Accordingly, paleoclimatic environmental fluctuations were shown to be an important factor affecting rodents in the subtropics of the Indo-Malayan region. Our results show that human activities during the last 10,000 years of the Holocene period affected the population dynamics of the rodent species examined, including introducing them to Myanmar from neighboring countries. Further study of these four commensal rodents in other geographic areas of the Indo-Malayan region would allow us to better understand the factors that drove their evolution and their ecological trends.
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14
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Etougbétché J, Houémènou G, Dossou HJ, Badou S, Gauthier P, Abdou Karim IY, Nicolas V, Dobigny G. Genetic diversity and origins of invasive black rats (Rattus rattus) in Benin, West Africa. JOURNAL OF VERTEBRATE BIOLOGY 2020. [DOI: 10.25225/jvb.20014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Jonas Etougbétché
- Ecole Polytechnique d'Abomey-Calavi, Laboratoire de Recherche en Biologie Appliquée, Unité de Recherche sur les Invasions Biologiques, Université d'Abomey-Calavi, Benin; e-mail: , , sylvestrebado
| | - Gualbert Houémènou
- Ecole Polytechnique d'Abomey-Calavi, Laboratoire de Recherche en Biologie Appliquée, Unité de Recherche sur les Invasions Biologiques, Université d'Abomey-Calavi, Benin; e-mail: , , sylvestrebado
| | - Henri-Joël Dossou
- Ecole Polytechnique d'Abomey-Calavi, Laboratoire de Recherche en Biologie Appliquée, Unité de Recherche sur les Invasions Biologiques, Université d'Abomey-Calavi, Benin; e-mail: , , sylvestrebado
| | - Sylvestre Badou
- Ecole Polytechnique d'Abomey-Calavi, Laboratoire de Recherche en Biologie Appliquée, Unité de Recherche sur les Invasions Biologiques, Université d'Abomey-Calavi, Benin; e-mail: , , sylvestrebado
| | - Philippe Gauthier
- Institut de Recherche pour le Développement, UMR CBGP IRD, INRA, Cirad, Institut SupAgro, Montpellier Université d'Excellence, France; e-mail: ;
| | - Issaka Youssao Abdou Karim
- Ecole Polytechnique d'Abomey-Calavi, Laboratoire de Biotechnologie Animale et de Technologie des Viandes, Université d'Abomey-Calavi, Benin; e-mail:
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB) Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 57 rue Cuvier, 75005 Paris, France; e-mail:
| | - Gauthier Dobigny
- Ecole Polytechnique d'Abomey-Calavi, Laboratoire de Recherche en Biologie Appliquée, Unité de Recherche sur les Invasions Biologiques, Université d'Abomey-Calavi, Benin; e-mail: , , sylvestrebado
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15
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van der Geer AA. Size matters: micro-evolution in Polynesian rats highlights body size changes as initial stage in evolution. PeerJ 2020; 8:e9076. [PMID: 32377457 PMCID: PMC7194086 DOI: 10.7717/peerj.9076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/07/2020] [Indexed: 12/03/2022] Open
Abstract
Microevolutionary patterns in populations of introduced rodent species have often been the focus of analytic studies for their potential relevance to understanding vertebrate evolution. The Polynesian rat (Rattus exulans) is an excellent proxy species because of its wide geographic and temporal distribution: its native and introduced combined range spans half the globe and it has been living for at least seven centuries wherever it was introduced. The objective of this study was to assess the effects of long-term isolation (insularity; up to 4,000 years) and geographic variables on skull shape variation using geometric morphometrics. A sample of 513 specimens from 103 islands and four mainland areas was analysed. This study, to my knowledge the first to extensively sample introduced rats, analysed 59 two-dimensional landmarks on the skull. Landmarks were obtained in three separate aspects (dorsal, lateral, ventral skull view). The coordinate data were then subjected to a multivariate ordination analysis (principal components analysis, or PCA), multivariate regressions, and a canonical variates analysis (CVA). Three measures of disparity were evaluated for each view. The results show that introduced Polynesian rats evolve skull shapes that conform to the general mammalian interspecific pattern of cranial evolutionary allometry (CREA), with proportionally longer snouts in larger specimens. In addition, larger skulls are more tubular in shape than the smaller skulls, which are more balloon-shaped with a rounder and wider braincase relative to those of large skulls. This difference is also observed between the sexes (sexual dimorphism), due to the slightly larger average male size. Large, tubular skulls with long snouts are typical for Polynesia and Remote Oceania, where no native mammals occur. The greater disparity of Polynesian rats on mammal species-poor islands ('exulans-only' region) provides further insight into how diversity may affect diversification through ecological release from predators and competitors.
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16
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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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17
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Abstract
Mice (Mus musculus) and rats (Rattus norvegicus) have long served as model systems for biomedical research. However, they are also excellent models for studying the evolution of populations, subspecies, and species. Within the past million years, they have spread in various waves across large parts of the globe, with the most recent spread in the wake of human civilization. They have developed into commensal species, but have also been able to colonize extreme environments on islands free of human civilization. Given that ample genomic and genetic resources are available for these species, they have thus also become ideal mammalian systems for evolutionary studies on adaptation and speciation, particularly in the combination with the rapid developments in population genomics. The chapter provides an overview of the systems and their history, as well as of available resources.
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Affiliation(s)
- Kristian K Ullrich
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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18
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van der Geer AAE. Effect of isolation on coat colour polymorphism of Polynesian rats in Island Southeast Asia and the Pacific. PeerJ 2019; 7:e6894. [PMID: 31119086 PMCID: PMC6511229 DOI: 10.7717/peerj.6894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 04/02/2019] [Indexed: 01/03/2023] Open
Abstract
Populations of vertebrate species introduced onto islands regularly develop similar phenotypic changes, e.g., larger or smaller body size, shortened limbs, duller coats, as well as behavioural changes such as increased tameness and reduced flight-initiation distance. These changes overlap in part with those associated with the 'domestication syndrome', especially tameness and changes in coat patterns, and might indicate a similar neural crest involvement in the concurrent development of multiple phenotypic traits. Here I examine long-term data on free-living populations of wild Polynesian rats from seven mainland countries and 117 islands (n = 3,034), covering the species' native and introduced range. Mainland populations showed no aberrant coat patterns, with the exception of one albino, whereas aberrant coat patterns were found in 12 island populations. Observed coat colour polymorphisms consisted of leucistic (including singular white patches), melanistic (darkly pigmented) and piebald (mixed) coat patterns. After isolation for at least seven centuries, wild Polynesian rat populations on islands seem to exhibit a trend towards a higher incidence of aberrant coat patterns. These phenotypic changes are here explained as a neutral, non-adaptive process, likely part of the 'domestication syndrome' (via the commensal pathway of domestication), in combination with genetic drift, little or no gene flow between the islands and/or the mainland and a relaxed selection (as a result of the weakening or removal of competitor/predator pressure) under commensality.
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19
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Zeng L, Ming C, Li Y, Su LY, Su YH, Otecko NO, Dalecky A, Donnellan S, Aplin K, Liu XH, Song Y, Zhang ZB, Esmailizadeh A, Sohrabi SS, Nanaei HA, Liu HQ, Wang MS, Ag Atteynine S, Rocamora G, Brescia F, Morand S, Irwin DM, Peng MS, Yao YG, Li HP, Wu DD, Zhang YP. Out of Southern East Asia of the Brown Rat Revealed by Large-Scale Genome Sequencing. Mol Biol Evol 2019; 35:149-158. [PMID: 29087519 DOI: 10.1093/molbev/msx276] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The geographic origin and migration of the brown rat (Rattus norvegicus) remain subjects of considerable debate. In this study, we sequenced whole genomes of 110 wild brown rats with a diverse world-wide representation. We reveal that brown rats migrated out of southern East Asia, rather than northern Asia as formerly suggested, into the Middle East and then to Europe and Africa, thousands of years ago. Comparison of genomes from different geographical populations reveals that many genes involved in the immune system experienced positive selection in the wild brown rat.
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Affiliation(s)
- Lin Zeng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Chen Ming
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming, China
| | - Ling-Yan Su
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, China
| | - Yan-Hua Su
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Ambroise Dalecky
- Institut de Recherche pour le Développement (Ird), CBGP (UMR INRA/IRD/Cirad/Montpellier SupAgro), Montferrier sur Lez cedex, France.,Institut de Recherche pour le Développement (Ird), LPED (UMR AMU/IRD), Marseille, France
| | - Stephen Donnellan
- University of Adelaide and the South Australian Museum, Adelaide, Australia
| | - Ken Aplin
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, DC
| | - Xiao-Hui Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ying Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhi-Bin Zhang
- State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Saeed S Sohrabi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Solimane Ag Atteynine
- Institut de Recherche pour le Développement (Ird), IMBE (UMR AMU/CNRS/IRD/UAPV), Bamako, Mali.,Faculté des Sciences et Techniques (FST), Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Gérard Rocamora
- Island Biodiversity & Conservation Center, University of Seychelles, Mahé, Seychelles
| | - Fabrice Brescia
- Diversité Biologique et Fonctionnelle des Ecosystèmes, Institut Agronomique néo-Calédonien, Port Laguerre, Paita, New Caledonia
| | - Serge Morand
- CNRS-CIRAD, Centre d'Infectiologie Christophe Mérieux du Laos, Vientiane, Lao PDR
| | - David M Irwin
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Ming-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Yong-Gang Yao
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, China
| | - Hai-Peng Li
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming, China
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20
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van der Geer AA. Changing Invaders: trends of gigantism in insular introduced rats. ENVIRONMENTAL CONSERVATION 2018; 45:203-211. [PMID: 35814732 PMCID: PMC7613022 DOI: 10.1017/s0376892918000085] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The degree and direction of morphological change in invasive species with a long history of introduction is insufficiently known for a larger scale than the archipelago or island group. Here, I analyse data for 105 island populations of Polynesian rats, Rattus exulans, covering the entirety of Oceania and Wallacea to test whether body size differs in insular populations and if so what biotic and abiotic features are correlated with it. All insular populations of this rat, except one, exhibit body sizes up to twice the size of their mainland conspecifics. Body size of insular populations is positively correlated with latitude, consistent with thermoregulatory predictions based on Bergmann's rule. Body size is negatively correlated with number of co-occurring mammalian species, confirming an ecological hypothesis of the island rule. The largest rats are found in the temperate zone of New Zealand as well as on mammalian species-poor islands of Polynesia and the Solomon Islands. Carnivory in the form of predation on nesting seabird colonies seems to promote 1.4- to 1.9-fold body size increases.
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21
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Wolf CA, Young HS, Zilliacus KM, Wegmann AS, McKown M, Holmes ND, Tershy BR, Dirzo R, Kropidlowski S, Croll DA. Invasive rat eradication strongly impacts plant recruitment on a tropical atoll. PLoS One 2018; 13:e0200743. [PMID: 30016347 PMCID: PMC6049951 DOI: 10.1371/journal.pone.0200743] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 05/22/2018] [Indexed: 11/19/2022] Open
Abstract
Rat eradication has become a common conservation intervention in island ecosystems and its effectiveness in protecting native vertebrates is increasingly well documented. Yet, the impacts of rat eradication on plant communities remain poorly understood. Here we compare native and non-native tree and palm seedling abundance before and after eradication of invasive rats (Rattus rattus) from Palmyra Atoll, Line Islands, Central Pacific Ocean. Overall, seedling recruitment increased for five of the six native trees species examined. While pre-eradication monitoring found no seedlings of Pisonia grandis, a dominant tree species that is important throughout the Pacific region, post-eradication monitoring documented a notable recruitment event immediately following eradication, with up to 688 individual P. grandis seedlings per 100m2 recorded one month post-eradication. Two other locally rare native trees with no observed recruitment in pre-eradication surveys had recruitment post-rat eradication. However, we also found, by five years post-eradication, a 13-fold increase in recruitment of the naturalized and range-expanding coconut palm Cocos nucifera. Our results emphasize the strong effects that a rat eradication can have on tree recruitment with expected long-term effects on canopy composition. Rat eradication released non-native C. nucifera, likely with long-term implications for community composition, potentially necessitating future management interventions. Eradication, nevertheless, greatly benefitted recruitment of native tree species. If this pattern persists over time, we expect long-term benefits for flora and fauna dependent on these native species.
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Affiliation(s)
- Coral A. Wolf
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
| | - Hillary S. Young
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Kelly M. Zilliacus
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Alexander S. Wegmann
- Botany Department, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Matthew McKown
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Nick D. Holmes
- Island Conservation, Santa Cruz, California, United States of America
| | - Bernie R. Tershy
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Rodolfo Dirzo
- Department of Biology, Stanford University, Stanford, California, United States of America
| | | | - Donald A. Croll
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, United States of America
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22
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Matisoo-Smith E. Genomics and Working with Indigenous Communities in the Pacific. AMERICAN ANTHROPOLOGIST 2018. [DOI: 10.1111/aman.13045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Abstract
To determine incidence and outcome of biliary atresia (BA) between ethnic groups in New Zealand (NZ), a retrospective review was undertaken of children with BA born between 2002 and 2014. Prioritized ethnicity was used to determine ethnicity and was compared to population data. Uni- and multivariate analyses were undertaken to determine demographic and biochemical factors associated with outcome. Overall incidence was 1 in 9181 (Māori 1 in 5285; European 1 in 16,228; P < 0.0001). Overall and transplant-free survival rates at 1, 2, and 5 years were 92%, 86%, 82% and 70%, 49%, 30% respectively with Māori having improved transplant-free survival (P < 0.05) despite European children undergoing Kasai earlier (49 vs 63 days). BA is more common in NZ than Europe and North America, which is attributable to a higher incidence in Māori but overall outcome is poorer. Māori have improved transplant-free survival compared to NZ European children but the reason is unknown.
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24
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Puckett EE, Park J, Combs M, Blum MJ, Bryant JE, Caccone A, Costa F, Deinum EE, Esther A, Himsworth CG, Keightley PD, Ko A, Lundkvist Å, McElhinney LM, Morand S, Robins J, Russell J, Strand TM, Suarez O, Yon L, Munshi-South J. Global population divergence and admixture of the brown rat (Rattus norvegicus). Proc Biol Sci 2017; 283:rspb.2016.1762. [PMID: 27798305 DOI: 10.1098/rspb.2016.1762] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 09/26/2016] [Indexed: 11/12/2022] Open
Abstract
Native to China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution. While black rats and the house mouse tracked the regional development of human agricultural settlements, brown rats did not appear in Europe until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade. We inferred the global phylogeography of brown rats using 32 k SNPs, and detected 13 evolutionary clusters within five expansion routes. One cluster arose following a southward expansion into Southeast Asia. Three additional clusters arose from two independent eastward expansions: one expansion from Russia to the Aleutian Archipelago, and a second to western North America. Westward expansion resulted in the colonization of Europe from which subsequent rapid colonization of Africa, the Americas and Australasia occurred, and multiple evolutionary clusters were detected. An astonishing degree of fine-grained clustering between and within sampling sites underscored the extent to which urban heterogeneity shaped genetic structure of commensal rodents. Surprisingly, few individuals were recent migrants, suggesting that recruitment into established populations is limited. Understanding the global population structure of R. norvegicus offers novel perspectives on the forces driving the spread of zoonotic disease, and aids in development of rat eradication programmes.
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Affiliation(s)
- Emily E Puckett
- Louis Calder Center, Biological Field Station, Fordham University, Armonk, NY 10504, USA
| | - Jane Park
- Louis Calder Center, Biological Field Station, Fordham University, Armonk, NY 10504, USA
| | - Matthew Combs
- Louis Calder Center, Biological Field Station, Fordham University, Armonk, NY 10504, USA
| | - Michael J Blum
- Xavier Center for Bioenvironmental Research, Tulane University, New Orleans, LA 70112, USA
| | | | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT 06520-8106, USA
| | - Federico Costa
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil
| | - Eva E Deinum
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK.,Mathematical and Statistical Methods Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Alexandra Esther
- Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests, Vertebrate Research, Julius Kühn Institute, Münster, Germany
| | - Chelsea G Himsworth
- Animal Health Centre, British Columbia Ministry of Agriculture, 1767 Angus Campbell Road, Abbotsford, British Columbia, Canada V3G 2M3
| | - Peter D Keightley
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Albert Ko
- Laboratory of Epidemiology and Public Health, Yale University, New Haven, CT, USA
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Lorraine M McElhinney
- Wildlife Zoonoses and Vector Borne Disease Research Group, Animal and Plant Health Agency (APHA), Woodham Lane, New Haw Surrey, UK
| | - Serge Morand
- CNRS-CIRAD, Centre d'Infectiologie Christophe Mérieux du Laos, Vientiane, Lao PDR
| | - Judith Robins
- Department of Anthropology, University of Auckland, Private Bag 92019, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - James Russell
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.,Department of Statistics, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Tanja M Strand
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Olga Suarez
- Laboratorio de Ecologia de Roedores Urbanos, IEGEBA-CONICET, EGE-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires Pabellon II, Ciudad Universitaria (C1428EHA), Buenos Aires, Argentina
| | - Lisa Yon
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Jason Munshi-South
- Louis Calder Center, Biological Field Station, Fordham University, Armonk, NY 10504, USA
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25
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Abstract
Homo sapiens phylogeography begins with the species' origin nearly 200 kya in Africa. First signs of the species outside Africa (in Arabia) are from 125 kya. Earliest dates elsewhere are now 100 kya in China, 45 kya in Australia and southern Europe (maybe even 60 kya in Australia), 32 kya in northeast Siberia, and maybe 20 kya in the Americas. Humans reached arctic regions and oceanic islands last-arctic North America about 5 kya, mid- and eastern Pacific islands about 2-1 kya, and New Zealand about 700 y ago. Initial routes along coasts seem the most likely given abundant and easily harvested shellfish there as indicated by huge ancient oyster shell middens on all continents. Nevertheless, the effect of geographic barriers-mountains and oceans-is clear. The phylogeographic pattern of diasporas from several single origins-northeast Africa to Eurasia, southeast Eurasia to Australia, and northeast Siberia to the Americas-allows the equivalent of a repeat experiment on the relation between geography and phylogenetic and cultural diversity. On all continents, cultural diversity is high in productive low latitudes, presumably because such regions can support populations of sustainable size in a small area, therefore allowing a high density of cultures. Of course, other factors operate. South America has an unusually low density of cultures in its tropical latitudes. A likely factor is the phylogeographic movement of peoples from the Old World bringing novel and hence, lethal diseases to the New World, a foretaste, perhaps, of present day global transport of tropical diseases.
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Llamas B, Willerslev E, Orlando L. Human evolution: a tale from ancient genomes. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0484. [PMID: 27994125 DOI: 10.1098/rstb.2015.0484] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2016] [Indexed: 12/21/2022] Open
Abstract
The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become a major player in the understanding of our evolutionary history.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Bastien Llamas
- Australian Centre for ADNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 K Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.,Wellcome Genome Campus Hinxton, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 K Copenhagen, Denmark .,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université de Toulouse, University Paul Sabatier, CNRS UMR 5288, 31000 Toulouse, France
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Woods R, Marr MM, Brace S, Barnes I. The Small and the Dead: A Review of Ancient DNA Studies Analysing Micromammal Species. Genes (Basel) 2017; 8:E312. [PMID: 29117125 PMCID: PMC5704225 DOI: 10.3390/genes8110312] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/13/2017] [Accepted: 10/13/2017] [Indexed: 02/06/2023] Open
Abstract
The field of ancient DNA (aDNA) has recently been in a state of exponential growth, largely driven by the uptake of Next Generation Sequencing (NGS) techniques. Much of this work has focused on the mammalian megafauna and ancient humans, with comparatively less studies looking at micromammal fauna, despite the potential of these species in testing evolutionary, environmental and taxonomic theories. Several factors make micromammal fauna ideally suited for aDNA extraction and sequencing. Micromammal subfossil assemblages often include the large number of individuals appropriate for population level analyses, and, furthermore, the assemblages are frequently found in cave sites where the constant temperature and sheltered environment provide favourable conditions for DNA preservation. This review looks at studies that include the use of aDNA in molecular analysis of micromammal fauna, in order to examine the wide array of questions that can be answered in the study of small mammals using new palaeogenetic techniques. This study highlights the bias in current aDNA studies and assesses the future use of aDNA as a tool for the study of micromammal fauna.
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Affiliation(s)
- Roseina Woods
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Melissa M Marr
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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Cole TL, Wood JR. The ancient DNA revolution: the latest era in unearthing New Zealand’s faunal history. NEW ZEALAND JOURNAL OF ZOOLOGY 2017. [DOI: 10.1080/03014223.2017.1376690] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Theresa L. Cole
- Department of Zoology, University of Otago, Dunedin, New Zealand
- Long Term Ecology Lab, Landcare Research, Lincoln, New Zealand
| | - Jamie R. Wood
- Long Term Ecology Lab, Landcare Research, Lincoln, New Zealand
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29
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Payacan C, Moncada X, Rojas G, Clarke A, Chung KF, Allaby R, Seelenfreund D, Seelenfreund A. Phylogeography of herbarium specimens of asexually propagated paper mulberry [Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae)] reveals genetic diversity across the Pacific. ANNALS OF BOTANY 2017; 120:387-404. [PMID: 28633358 PMCID: PMC5591419 DOI: 10.1093/aob/mcx062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/16/2017] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Paper mulberry or Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae) is a dioecious species native to continental South-east Asia and East Asia, including Taiwan, that was introduced to the Pacific by pre-historic voyagers and transported intentionally and propagated asexually across the full range of Austronesian expansion from Taiwan to East Polynesia. The aim of this study was to gain insight into the dispersal of paper mulberry into Oceania through the genetic analysis of herbaria samples which represent a more complete coverage of the historical geographical range of the species in the Pacific before later introductions and local extinctions occurred. METHODS DNA from 47 herbarium specimens of B. papyrifera collected from 1882 to 2006 from different islands of the Pacific was obtained under ancient DNA protocols. Genetic characterization was based on the ribosomal internal transcribed spacer ITS-1 sequence, a sex marker, the chloroplast ndhF-rpl32 intergenic spacer and a set of ten microsatellites developed for B. papyrifera. KEY RESULTS Microsatellites allowed detection of 15 genotypes in Near and Remote Oceanian samples, in spite of the vegetative propagation of B. papyrifera in the Pacific. These genotypes are structured in two groups separating West and East Polynesia, and place Pitcairn in a pivotal position. We also detected the presence of male plants that carry the Polynesian chloroplast DNA (cpDNA) haplotype, in contrast to findings in contemporary B. papyrifera populations where only female plants bear the Polynesian cpDNA haplotype. CONCLUSIONS For the first time, genetic diversity was detected among paper mulberry accessions from Remote Oceania. A clear separation between West and East Polynesia was found that may be indicative of pulses during its dispersal history. The pattern linking the genotypes within Remote Oceania reflects the importance of central Polynesia as a dispersal hub, in agreement with archaeological evidence.
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Affiliation(s)
- Claudia Payacan
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Ximena Moncada
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), La Serena, Chile
| | - Gloria Rojas
- Museo Nacional de Historia Natural, Santiago, Chile
| | - Andrew Clarke
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Kuo-Fang Chung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan and
| | - Robin Allaby
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Daniela Seelenfreund
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Andrea Seelenfreund
- Escuela de Antropología, Universidad Academia de Humanismo Cristiano, Santiago, Chile
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Rodent-borne Trypanosoma from cities and villages of Niger and Nigeria: A special role for the invasive genus Rattus? Acta Trop 2017; 171:151-158. [PMID: 28373037 DOI: 10.1016/j.actatropica.2017.03.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/17/2017] [Accepted: 03/27/2017] [Indexed: 12/11/2022]
Abstract
Although they are known to sometimes infect humans, atypical trypanosomes are very poorly documented, especially in Africa where one lethal case has yet been described. Here we conducted a survey of rodent-borne Trypanosoma in 19 towns and villages of Niger and Nigeria, with a special emphasis on Niamey, the capital city of Niger. The 1298 rodents that were captured yielded 189 qPCR-positive animals from 14 localities, thus corresponding to a 14.6% overall prevalence. Rats, especially black rats, displayed particularly elevated prevalence (27.4%), with some well sampled sites showing 40-50% and up to 68.8% of Trypanosoma-carrying individuals. Rattus were also characterized by significantly lower Ct values than in the other non-Rattus species. DNA sequences could be obtained for 43 rodent-borne Trypanosoma and corresponded to 41 T. lewisi (all from Rattus) and 2 T. microti (from Cricetomys gambianus). These results, together with data compiled from the available literature, suggest that Rattus may play a particular role for the maintaining and circulation of Trypanosoma, especially T. lewisi, in Africa. Taken into account its strong abilities to invade coastal and inland regions of the continent, we believe that this genus deserves a particular attention in regards to potentially under-looked but emerging atypical trypanosome-related diseases.
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West K, Collins C, Kardailsky O, Kahn J, Hunt TL, Burley DV, Matisoo-Smith E. The Pacific Rat Race to Easter Island: Tracking the Prehistoric Dispersal of Rattus exulans Using Ancient Mitochondrial Genomes. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00052] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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Young H, Miller-ter Kuile A, McCauley D, Dirzo R. Cascading community and ecosystem consequences of introduced coconut palms ( Cocos nucifera) in tropical islands. CAN J ZOOL 2017. [DOI: 10.1139/cjz-2016-0107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Biological invasions are a pervasive and dominant form of anthropogenic disturbance. However, we seldom have the opportunity to evaluate the long-term, indirect, and often slow-moving cascading effects of invasions at the community and ecosystem scale. Here we synthesize the collective knowledge from 10 years of study on the influence of the deep historical introduction of coconut palms (Cocos nucifera L.) across a series of islets at Palmyra Atoll. Through a suite of pathways, we find this palm drives near-complete ecosystem state change when it becomes dominant. Abiotic conditions are transformed, with major soil nutrients 2.7–11.5 times lower and water stress 15% elevated in palm-dominated forests compared with native forest. Faunal communities are likewise dramatically altered, not only in composition but also in behavior, body size, and body condition. Biotic interactions, including herbivory rates, palatability, and seed predation, are likewise changed. Cumulatively, these changes transform food webs, leading to dramatically shortened and simplified food chains in invaded ecosystems. Many of these changes appear to create slow-acting feedback loops that favor the palm at the expense of native species. Given the widespread nature of this historical introduction, many island and coastal regions of tropical oceans may be similarly transformed.
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Affiliation(s)
- H.S. Young
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - A. Miller-ter Kuile
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - D.J. McCauley
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - R. Dirzo
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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33
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Brown PR, Aplin KP, Hinds LA, Jacob J, Thomas SE, Ritchie BJ. Rodent management issues in South Pacific islands: a review with case studies from Papua New Guinea and Vanuatu. WILDLIFE RESEARCH 2017. [DOI: 10.1071/wr17104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Rodents are a key pest to agricultural and rural island communities of the South Pacific, but there is limited information of their impact on the crops and livelihoods of small-scale farmers. The rodent pest community is known, but the type and scales of damage to different crops on different islands are unknown. Knowledge about rodent pest management in other geographical regions may not be directly transferable to the Pacific region. Many studies on islands have largely focussed on the eradication of rodents from uninhabited islands for conservation benefits. These broadscale eradication efforts are unlikely to translate to inhabited islands because of complex social and agricultural issues. The livelihoods, culture and customs of poor small-scale farmers in the South Pacific have a large bearing on the current management of rodents. The aim of the present review was to describe the rodent problems, impacts and management of rodents on South Pacific islands, and identify gaps for further research. We compared and contrasted two case studies. The situation in Papua New Guinea is emergent as several introduced rodent species are actively invading new areas with wide-ranging implications for human livelihoods and conservation. In Vanuatu, we show how rodent damage on cocoa plantations can be reduced by good orchard hygiene through pruning and weeding, which also has benefits for the management of black pod disease. We conclude that (1) damage levels are unknown and unreported, (2) the impacts on human health are unknown, (3) the relationships between the pest species and their food sources, breeding and movements are not known, and (4) the situation in Papua New Guinea may represent an emergent crisis that warrants further investigation. In addition, there is a need for greater understanding of the invasive history of pest rodents, so as to integrate biological information with management strategies. Ecologically based rodent management can be achieved on Pacific Islands, but only after significant well funded large-scale projects are established and rodent ecologists are trained. We can learn from experiences from other locations such as Southeast Asia to guide the way.
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Fleming PJS, Ballard G, Reid NCH, Tracey JP. Invasive species and their impacts on agri-ecosystems: issues and solutions for restoring ecosystem processes. RANGELAND JOURNAL 2017. [DOI: 10.1071/rj17046] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Humans are the most invasive of vertebrates and they have taken many plants and animals with them to colonise new environments. This has been particularly so in Australasia, where Laurasian and domesticated taxa have collided with ancient Gondwanan ecosystems isolated since the Eocene Epoch. Many plants and animals that humans introduced benefited from their pre-adaptation to their new environments and some became invasive, damaging the biodiversity and agricultural value of the invaded ecosystems. The invasion of non-native organisms is accelerating with human population growth and globalisation. Expansion of trade has seen increases in purposeful and accidental introductions, and their negative impacts are regarded as second only to activities associated with human population growth. Here, the theoretical processes, economic and environmental costs of invasive alien species (i.e. weeds and vertebrate pests) are outlined. However, defining the problem is only one side of the coin. We review some theoretical underpinnings of invasive species science and management, and discuss hypotheses to explain successful biological invasions. We consider desired restoration states and outline a practical working framework for managing invasive plants and animals to restore, regenerate and revegetate invaded Australasian ecosystems.
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35
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Using seafaring simulations and shortest-hop trajectories to model the prehistoric colonization of Remote Oceania. Proc Natl Acad Sci U S A 2016; 113:12685-12690. [PMID: 27791145 DOI: 10.1073/pnas.1612426113] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The prehistoric colonization of islands in Remote Oceania that began ∼3400 B.P. represents what was arguably the most expansive and ambitious maritime dispersal of humans across any of the world's seas or oceans. Though archaeological evidence has provided a relatively clear picture of when many of the major island groups were colonized, there is still considerable debate as to where these settlers originated from and their strategies/trajectories used to reach habitable land that other datasets (genetic, linguistic) are also still trying to resolve. To address these issues, we have harnessed the power of high-resolution climatic and oceanographic datasets in multiple seafaring simulation platforms to examine major pulses of colonization in the region. Our analysis, which takes into consideration currents, land distribution, wind periodicity, the influence of El Niño Southern Oscillation (ENSO) events, and "shortest-hop" trajectories, demonstrate that (i) seasonal and semiannual climatic changes were highly influential in structuring ancient Pacific voyaging; (ii) western Micronesia was likely settled from somewhere around the Maluku (Molucca) Islands; (iii) Samoa was the most probable staging area for the colonization of East Polynesia; and (iv) although there are major differences in success rates depending on time of year and the occurrence of ENSO events, settlement of Hawai'i and New Zealand is possible from the Marquesas or Society Islands, the same being the case for settlement of Easter Island from Mangareva or the Marquesas.
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36
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Morand S, Bordes F, Chen HW, Claude J, Cosson JF, Galan M, Czirják GÁ, Greenwood AD, Latinne A, Michaux J, Ribas A. Global parasite and Rattus rodent invasions: The consequences for rodent-borne diseases. Integr Zool 2016; 10:409-23. [PMID: 26037785 DOI: 10.1111/1749-4877.12143] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We summarize the current knowledge on parasitism-related invasion processes of the globally invasive Rattus lineages, originating from Asia, and how these invasions have impacted the local epidemiology of rodent-borne diseases. Parasites play an important role in the invasion processes and successes of their hosts through multiple biological mechanisms such as "parasite release," "immunocompetence advantage," "biotic resistance" and "novel weapon." Parasites may also greatly increase the impact of invasions by spillover of parasites and other pathogens, introduced with invasive hosts, into new hosts, potentially leading to novel emerging diseases. Another potential impact is the ability of the invader to amplify local parasites by spillback. In both cases, local fauna and humans may be exposed to new health risks, which may decrease biodiversity and potentially cause increases in human morbidity and mortality. Here we review the current knowledge on these processes and propose some research priorities.
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Affiliation(s)
- Serge Morand
- Centre National de la Recherche Scientifique (CNRS)-Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) Animal et Gestion Intégrée des Risques, Centre d'Infectiologie Christophe Mérieux du Laos, Vientiane, Lao PDR.,Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Frédéric Bordes
- Institut des Sciences de l'Evolution, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier-Institut de Recherche pour le Développement (IRD), Montpellier, France
| | - Hsuan-Wien Chen
- Department of Biological Resources, National Chiayi University, Chiayi City, Taiwan, China
| | - Julien Claude
- Institut des Sciences de l'Evolution, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier-Institut de Recherche pour le Développement (IRD), Montpellier, France
| | - Jean-François Cosson
- Institut National de la Recherche Agronomique (INRA), Centre de Biologie et de Gestion des Populations, Baillarguet, France.,Institut National de la Recherche Agronomique (INRA), UMR Biologie et Immunologie Parasitaire Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail ses, Maisons-Alfort, France
| | - Maxime Galan
- Institut National de la Recherche Agronomique (INRA), Centre de Biologie et de Gestion des Populations, Baillarguet, France
| | - Gábor Á Czirják
- Leibniz Institute for Zoo and Wildlife Research, Department of Wildlife Diseases, 10315 Berlin, Germany
| | - Alex D Greenwood
- Leibniz Institute for Zoo and Wildlife Research, Department of Wildlife Diseases, 10315 Berlin, Germany
| | - Alice Latinne
- Institut des Sciences de l'Evolution, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier-Institut de Recherche pour le Développement (IRD), Montpellier, France.,Conservation Genetics Unit, University of Liège 4000 Liège, Belgium
| | - Johan Michaux
- Centre National de la Recherche Scientifique (CNRS)-Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) Animal et Gestion Intégrée des Risques, Centre d'Infectiologie Christophe Mérieux du Laos, Vientiane, Lao PDR.,Conservation Genetics Unit, University of Liège 4000 Liège, Belgium
| | - Alexis Ribas
- Biodiversity Research Group, Faculty of Science, Udon Thani Rajabhat University, Udon Thani, Thailand
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Timm RM, Weijola V, Aplin KP, Donnellan SC, Flannery TF, Thomson V, Pine RH. A new species ofRattus(Rodentia: Muridae) from Manus Island, Papua New Guinea. J Mammal 2016. [DOI: 10.1093/jmammal/gyw034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Global divergence of the human follicle mite Demodex folliculorum: Persistent associations between host ancestry and mite lineages. Proc Natl Acad Sci U S A 2015; 112:15958-63. [PMID: 26668374 DOI: 10.1073/pnas.1512609112] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microscopic mites of the genus Demodex live within the hair follicles of mammals and are ubiquitous symbionts of humans, but little molecular work has been done to understand their genetic diversity or transmission. Here we sampled mite DNA from 70 human hosts of diverse geographic ancestries and analyzed 241 sequences from the mitochondrial genome of the species Demodex folliculorum. Phylogenetic analyses recovered multiple deep lineages including a globally distributed lineage common among hosts of European ancestry and three lineages that primarily include hosts of Asian, African, and Latin American ancestry. To a great extent, the ancestral geography of hosts predicted the lineages of mites found on them; 27% of the total molecular variance segregated according to the regional ancestries of hosts. We found that D. folliculorum populations are stable on an individual over the course of years and that some Asian and African American hosts maintain specific mite lineages over the course of years or generations outside their geographic region of birth or ancestry. D. folliculorum haplotypes were much more likely to be shared within families and between spouses than between unrelated individuals, indicating that transmission requires close contact. Dating analyses indicated that D. folliculorum origins may predate modern humans. Overall, D. folliculorum evolution reflects ancient human population divergences, is consistent with an out-of-Africa dispersal hypothesis, and presents an excellent model system for further understanding the history of human movement.
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Kosoy M, Khlyap L, Cosson JF, Morand S. Aboriginal and invasive rats of genus Rattus as hosts of infectious agents. Vector Borne Zoonotic Dis 2015; 15:3-12. [PMID: 25629775 DOI: 10.1089/vbz.2014.1629] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
From the perspective of ecology of zoonotic pathogens, the role of the Old World rats of the genus Rattus is exceptional. The review analyzes specific characteristics of rats that contribute to their important role in hosting pathogens, such as host-pathogen relations and rates of rat-borne infections, taxonomy, ecology, and essential factors. Specifically the review addresses recent taxonomic revisions within the genus Rattus that resulted from applications of new genetic tools in understanding relationships between the Old World rats and the infectious agents that they carry. Among the numerous species within the genus Rattus, only three species-the Norway rat (R. norvegicus), the black or roof rat (R. rattus), and the Asian black rat (R. tanezumi)-have colonized urban ecosystems globally for a historically long period of time. The fourth invasive species, R. exulans, is limited to tropical Asia-Pacific areas. One of the points highlighted in this review is the necessity to discriminate the roles played by rats as pathogen reservoirs within the land of their original diversification and in regions where only one or few rat species were introduced during the recent human history.
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Affiliation(s)
- Michael Kosoy
- 1 Centers for Disease Control and Prevention , Division of Vector-Borne Diseases, Fort Collins, Colorado
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40
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Tracking Austronesian expansion into the Pacific via the paper mulberry plant. Proc Natl Acad Sci U S A 2015; 112:13432-3. [PMID: 26499243 DOI: 10.1073/pnas.1518576112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Greig K, Boocock J, Prost S, Horsburgh KA, Jacomb C, Walter R, Matisoo-Smith E. Complete Mitochondrial Genomes of New Zealand's First Dogs. PLoS One 2015; 10:e0138536. [PMID: 26444283 PMCID: PMC4596854 DOI: 10.1371/journal.pone.0138536] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 09/01/2015] [Indexed: 11/25/2022] Open
Abstract
Dogs accompanied people in their migrations across the Pacific Ocean and ultimately reached New Zealand, which is the southern-most point of their oceanic distribution, around the beginning of the fourteenth century AD. Previous ancient DNA analyses of mitochondrial control region sequences indicated the New Zealand dog population included two lineages. We sequenced complete mitochondrial genomes of fourteen dogs from the colonisation era archaeological site of Wairau Bar and found five closely-related haplotypes. The limited number of mitochondrial lineages present at Wairau Bar suggests that the founding population may have comprised only a few dogs; or that the arriving dogs were closely related. For populations such as that at Wairau Bar, which stemmed from relatively recent migration events, control region sequences have insufficient power to address questions about population structure and founding events. Sequencing mitogenomes provided the opportunity to observe sufficient diversity to discriminate between individuals that would otherwise be assigned the same haplotype and to clarify their relationships with each other. Our results also support the proposition that at least one dispersal of dogs into the Pacific was via a south-western route through Indonesia.
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Affiliation(s)
- Karen Greig
- Allan Wilson Centre, Department of Anatomy, University of Otago, Dunedin, New Zealand
- Department of Anthropology and Archaeology, University of Otago, Dunedin, New Zealand
- * E-mail: (KG); (EMS)
| | - James Boocock
- Allan Wilson Centre, Department of Anatomy, University of Otago, Dunedin, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Stefan Prost
- Allan Wilson Centre, Department of Anatomy, University of Otago, Dunedin, New Zealand
- Department of Integrative Biology, University of California, Berkeley, United States of America
| | - K. Ann Horsburgh
- Department of Anthropology, Southern Methodist University, Dallas, United States of America
- School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa
| | - Chris Jacomb
- Department of Anthropology and Archaeology, University of Otago, Dunedin, New Zealand
| | - Richard Walter
- Department of Anthropology and Archaeology, University of Otago, Dunedin, New Zealand
| | - Elizabeth Matisoo-Smith
- Allan Wilson Centre, Department of Anatomy, University of Otago, Dunedin, New Zealand
- * E-mail: (KG); (EMS)
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A holistic picture of Austronesian migrations revealed by phylogeography of Pacific paper mulberry. Proc Natl Acad Sci U S A 2015; 112:13537-42. [PMID: 26438853 DOI: 10.1073/pnas.1503205112] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The peopling of Remote Oceanic islands by Austronesian speakers is a fascinating and yet contentious part of human prehistory. Linguistic, archaeological, and genetic studies have shown the complex nature of the process in which different components that helped to shape Lapita culture in Near Oceania each have their own unique history. Important evidence points to Taiwan as an Austronesian ancestral homeland with a more distant origin in South China, whereas alternative models favor South China to North Vietnam or a Southeast Asian origin. We test these propositions by studying phylogeography of paper mulberry, a common East Asian tree species introduced and clonally propagated since prehistoric times across the Pacific for making barkcloth, a practical and symbolic component of Austronesian cultures. Using the hypervariable chloroplast ndhF-rpl32 sequences of 604 samples collected from East Asia, Southeast Asia, and Oceanic islands (including 19 historical herbarium specimens from Near and Remote Oceania), 48 haplotypes are detected and haplotype cp-17 is predominant in both Near and Remote Oceania. Because cp-17 has an unambiguous Taiwanese origin and cp-17-carrying Oceanic paper mulberries are clonally propagated, our data concur with expectations of Taiwan as the Austronesian homeland, providing circumstantial support for the "out of Taiwan" hypothesis. Our data also provide insights into the dispersal of paper mulberry from South China "into North Taiwan," the "out of South China-Indochina" expansion to New Guinea, and the geographic origins of post-European introductions of paper mulberry into Oceania.
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Abstract
Our understanding of human evolutionary and population history can be advanced by ecological and evolutionary studies of our parasites. Many parasites flourish only in the presence of very specific human behaviors and in specific habitats, are wholly dependent on us, and have evolved with us for thousands or millions of years. Therefore, by asking when and how we first acquired those parasites, under which environmental and cultural conditions we are the most susceptible, and how the parasites have evolved and adapted to us and we in response to them, we can gain considerable insight into our own evolutionary history. As examples, the tapeworm life cycle is dependent on our consumption of meat, the divergence of body and head lice may have been subsequent to the development of clothing, and malaria hyperendemicity may be associated with agriculture. Thus, the evolutionary and population histories of these parasites are likely intertwined with critical aspects of human biology and culture. Here I review the mechanics of these and multiple other parasite proxies for human evolutionary history and discuss how they currently complement our fossil, archeological, molecular, linguistic, historical, and ethnographic records. I also highlight potential future applications of this promising model for the field of evolutionary anthropology.
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Brandt G, Merico A. The slow demise of Easter Island: insights from a modeling investigation. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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45
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Harper GA, Bunbury N. Invasive rats on tropical islands: Their population biology and impacts on native species. Glob Ecol Conserv 2015. [DOI: 10.1016/j.gecco.2015.02.010] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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46
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Matisoo-Smith E. Ancient DNA and the human settlement of the Pacific: a review. J Hum Evol 2015; 79:93-104. [PMID: 25556846 DOI: 10.1016/j.jhevol.2014.10.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 09/01/2014] [Accepted: 10/28/2014] [Indexed: 11/30/2022]
Abstract
The Pacific region provides unique opportunities to study human evolution including through analyses of ancient DNA. While some of the earliest studies involving ancient DNA from skeletal remains focused on Pacific samples, in the following 25 years, several factors meant that little aDNA research, particularly research focused on human populations, has emerged. This paper briefly presents the genetic evidence for population origins, reviews what ancient DNA work has been undertaken to address human history and evolution in the Pacific region, and argues that the future is bright but research requires a collaborative approach between academic disciplines but also with local communities.
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Affiliation(s)
- Elizabeth Matisoo-Smith
- Department of Anatomy and Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, PO Box 913, Dunedin 9054, New Zealand.
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47
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Witt KE, Judd K, Kitchen A, Grier C, Kohler TA, Ortman SG, Kemp BM, Malhi RS. DNA analysis of ancient dogs of the Americas: identifying possible founding haplotypes and reconstructing population histories. J Hum Evol 2014; 79:105-18. [PMID: 25532803 DOI: 10.1016/j.jhevol.2014.10.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 06/16/2014] [Accepted: 10/22/2014] [Indexed: 11/13/2022]
Abstract
As dogs have traveled with humans to every continent, they can potentially serve as an excellent proxy when studying human migration history. Past genetic studies into the origins of Native American dogs have used portions of the hypervariable region (HVR) of mitochondrial DNA (mtDNA) to indicate that prior to European contact the dogs of Native Americans originated in Eurasia. In this study, we summarize past DNA studies of both humans and dogs to discuss their population histories in the Americas. We then sequenced a portion of the mtDNA HVR of 42 pre-Columbian dogs from three sites located in Illinois, coastal British Columbia, and Colorado, and identify four novel dog mtDNA haplotypes. Next, we analyzed a dataset comprised of all available ancient dog sequences from the Americas to infer the pre-Columbian population history of dogs in the Americas. Interestingly, we found low levels of genetic diversity for some populations consistent with the possibility of deliberate breeding practices. Furthermore, we identified multiple putative founding haplotypes in addition to dog haplotypes that closely resemble those of wolves, suggesting admixture with North American wolves or perhaps a second domestication of canids in the Americas. Notably, initial effective population size estimates suggest at least 1000 female dogs likely existed in the Americas at the time of the first known canid burial, and that population size increased gradually over time before stabilizing roughly 1200 years before present.
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Affiliation(s)
- Kelsey E Witt
- School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Kathleen Judd
- Kemp Lab of Molecular Anthropology and Ancient DNA, Washington State University, Pullman, WA 99164, USA
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, IA 52242, USA
| | - Colin Grier
- Department of Anthropology, Washington State University, Pullman, WA 99164, USA
| | - Timothy A Kohler
- Department of Anthropology, Washington State University, Pullman, WA 99164, USA; Santa Fe Institute, Santa Fe, NM 87501, USA; Crow Canyon Archaeological Center, 23390 Road K, Cortez, CO 81321-9408, USA
| | - Scott G Ortman
- Department of Anthropology, University of Colorado, Boulder, CO 80309, USA
| | - Brian M Kemp
- Department of Anthropology, Washington State University, Pullman, WA 99164, USA; School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Ripan S Malhi
- School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology and Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA.
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48
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Kundu S, Ghosh SK. Trend of different molecular markers in the last decades for studying human migrations. Gene 2014; 556:81-90. [PMID: 25510397 DOI: 10.1016/j.gene.2014.12.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 12/07/2014] [Accepted: 12/11/2014] [Indexed: 12/15/2022]
Abstract
Anatomically modern humans are known to have widely migrated throughout history. Different scientific evidences suggest that the entire human population descended from just several thousand African migrants. About 85,000 years ago, the first wave of human migration was out of Africa, that followed the coasts through the Middle East, into Southern Asia via Sri Lanka, and in due course around Indonesia and into Australia. Another wave of migration between 40,000 and 12,000 years ago brought humans northward into Europe. However, the frozen north limited human expansion in Europe, and created a land bridge, "Bering land bridge", connecting Asia with North America about 25,000 years ago. Although fossil data give the most direct information about our past, it has certain anomalies. So, molecular archeologists are now using different molecular markers to trace the "most recent common ancestor" and also the migration pattern of modern humans. In this study, we have studied the trend of molecular markers and also the methodologies implemented in the last decades (2003-2014). From our observation, we can say that D-loop region of mtDNA and Y chromosome based markers are predominant. Nevertheless, mtDNA, especially the D-loop region, has some unique features, which makes it a more effective marker for tracing prehistoric footprints of modern human populations. Although, natural selection should also be taken into account in studying mtDNA based human migration. As per technology is concerned, Sanger sequencing is the major technique that is being used in almost all studies. But, the emergence of different cost-effective-and-easy-to-handle NGS platforms has increased its popularity over Sanger sequencing in studying human migration.
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Affiliation(s)
- Sharbadeb Kundu
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Pin-788011 Assam, India
| | - Sankar Kumar Ghosh
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Pin-788011 Assam, India.
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Garba M, Dalecky A, Kadaoure I, Kane M, Hima K, Veran S, Gagare S, Gauthier P, Tatard C, Rossi JP, Dobigny G. Spatial segregation between invasive and native commensal rodents in an urban environment: a case study in Niamey, Niger. PLoS One 2014; 9:e110666. [PMID: 25379785 PMCID: PMC4224371 DOI: 10.1371/journal.pone.0110666] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/22/2014] [Indexed: 11/19/2022] Open
Abstract
Invasive rodents have been responsible for the diffusion worldwide of many zoonotic agents, thus representing major threats for public health. Cities are important hubs for people and goods exchange and are thus expected to play a pivotal role in invasive commensal rodent dissemination. Yet, data about urban rodents' ecology, especially invasive vs. native species interactions, are dramatically scarce. Here, we provide results of an extensive survey of urban rodents conducted in Niamey, Niger, depicting the early stages of rodent bioinvasions within a city. We explore the species-specific spatial distributions throughout the city using contrasted approaches, namely field sampling, co-occurrence analysis, occupancy modelling and indicator geostatistics. We show that (i) two species (i.e. rural-like vs. truly commensal) assemblages can be identified, and that (ii) within commensal rodents, invasive (Rattus rattus and Mus musculus) and native (Mastomys natalensis) species are spatially segregated. Moreover, several pieces of arguments tend to suggest that these exclusive distributions reflect an ongoing native-to-invasive species turn over. The underlying processes as well as the possible consequences for humans are discussed.
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Affiliation(s)
- Madougou Garba
- Centre Régional Agrhymet, Département Formation Recherche, Niamey, Niger
- Université Abdou Moumouni, Faculté des Sciences, Niamey, Niger
- Direction Générale de la Protection des Végétaux, Ministère de l′Agriculture, Niamey, Niger
| | - Ambroise Dalecky
- IRD, Aix Marseille Université, LPED (UMR IRD-AMU), Marseille, France
- IRD, CBGP (UMR IRD-INRA-Cirad-SupAgro Montpellier), Campus International de Baillarguet, Montferrier-sur-Lez, France
| | | | - Mamadou Kane
- IRD, CBGP, Campus ISRA-IRD de Dakar-Bel-Air, Dakar, Senegal
| | - Karmadine Hima
- Université Abdou Moumouni, Faculté des Sciences, Niamey, Niger
| | - Sophie Veran
- INRA, CBGP, Campus International de Baillarguet, Montferrier-sur-Lez, France
| | - Sama Gagare
- Centre Régional Agrhymet, Département Formation Recherche, Niamey, Niger
| | - Philippe Gauthier
- IRD, CBGP (UMR IRD-INRA-Cirad-SupAgro Montpellier), Campus International de Baillarguet, Montferrier-sur-Lez, France
| | - Caroline Tatard
- INRA, CBGP, Campus International de Baillarguet, Montferrier-sur-Lez, France
| | - Jean-Pierre Rossi
- INRA, CBGP, Campus International de Baillarguet, Montferrier-sur-Lez, France
| | - Gauthier Dobigny
- Centre Régional Agrhymet, Département Formation Recherche, Niamey, Niger
- IRD, CBGP (UMR IRD-INRA-Cirad-SupAgro Montpellier), Campus International de Baillarguet, Montferrier-sur-Lez, France
- * E-mail:
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50
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Jing M, Yu HT, Bi X, Lai YC, Jiang W, Huang L. Phylogeography of Chinese house mice (Mus musculus musculus/castaneus): distribution, routes of colonization and geographic regions of hybridization. Mol Ecol 2014; 23:4387-405. [PMID: 25065953 DOI: 10.1111/mec.12873] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 07/22/2014] [Accepted: 07/23/2014] [Indexed: 11/27/2022]
Abstract
House mice (Mus musculus) are human commensals and have served as a primary model in biomedical, ecological and evolutionary research. Although there is detailed knowledge of the biogeography of house mice in Europe, little is known of the history of house mice in China, despite the fact that China encompasses an enormous portion of their range. In the present study, 535 house mice caught from 29 localities in China were studied by sequencing the mitochondrial D-loop and genotyping 10 nuclear microsatellite markers distributed on 10 chromosomes. Phylogenetic analyses revealed two evolutionary lineages corresponding to Mus musculus castaneus and Mus musculus musculus in the south and north, respectively, with the Yangtze River approximately representing the boundary. More detailed analyses combining published sequence data from mice sampled in neighbouring countries revealed the migration routes of the two subspecies into China: M. m. castaneus appeared to have migrated through a southern route (Yunnan and Guangxi), whereas M. m. musculus entered China from Kazakhstan through the north-west border (Xinjiang). Bayesian analysis of mitochondrial sequences indicated rapid population expansions in both subspecies, approximately 4650-9300 and 7150-14 300 years ago for M. m. castaneus and M. m. musculus, respectively. Interestingly, the migration routes of Chinese house mice coincide with the colonization routes of modern humans into China, and the expansion times of house mice are consistent with the development of agriculture in southern and northern China, respectively. Finally, our study confirmed the existence of a hybrid zone between M. m. castaneus and M. m. musculus in China. Further study of this hybrid zone will provide a useful counterpart to the well-studied hybrid zone between M. m. musculus and Mus musculus domesticus in central Europe.
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Affiliation(s)
- Meidong Jing
- College of Life Sciences, Ludong University, Yantai, Shandong, 264025, China
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