101
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Ko BJ, An J, Eo SH. Korean Leopard Cat (Prionailurus bengalensis) population with low genetic diversity is distinct from Southeast Asian populations. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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102
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Wei S, Sun S, Dou H, An F, Gao H, Guo C, Hua Y. Influence of Pleistocene climate fluctuations on the demographic history and distribution of the critically endangered Chinese pangolin (Manis pentadactyla). BMC ZOOL 2022; 7:50. [PMID: 37170389 PMCID: PMC10127079 DOI: 10.1186/s40850-022-00153-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 08/24/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Pleistocene climate fluctuations have strongly modified species genetic diversity and distributions. The Chinese pangolin (Manis pentadactyla) has been recognized as a critically endangered animal due to heavy poaching and trafficking. However, the effect of Pleistocene climate fluctuations on the genetic diversity and spatial distribution of the Chinese pangolin remains largely unknown. Here, we combined whole genome sequencing data, analysis of complete mitochondrial genomes, and a large amount of occurrence data from field surveys to infer the ancestral demographic history and predict the past spatial dynamics of the Chinese pangolin in Guangdong Province, China.
Results
Our results indicated that there were two subpopulations, which showed similar trends of population size change in response to past climatic changes. We estimated a peak effective population size (Ne) during the last interglacial (LIG), followed by a marked decrease (~ 0.5 to fivefold change) until the last glacial maximum (LGM) and a rebound to a small peak population size during the Mid-Holocene (MH). The estimated time of the separation event between two subpopulations was approximately 3,000–2,500 years ago (ka). We estimated that the distribution of suitable areas shrank by 14.4% from the LIG to LGM, followed by an expansion of 31.4% from the LGM to MH and has been stable since then. In addition, we identified an elevational shift and suitable area decreased significantly during the LGM, but that the geographic extent of suitable areas in the western region increased from the LIG to present. The eastern region of Guangdong Province had the highest habitat suitability across all the climate scenarios.
Conclusions
Our results suggested that Pleistocene climate fluctuations played an important role in shaping patterns of genetic diversity and spatial distribution, and that human stressors likely contributed to the recent divergence of two Chinese pangolin subpopulations sampled here. We argue that a key protected area should be established in the eastern region of Guangdong Province. As such, this study provides a more thorough understanding of the impacts of Pleistocene climate fluctuations impacts on a mammalian species in southern China and suggests more robust management and conservation plans for this Critically Endangered species of special interest.
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103
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Across the Gobi Desert: impact of landscape features on the biogeography and phylogeographically-structured release calls of the Mongolian Toad, Strauchbufo raddei in East Asia. Evol Ecol 2022. [DOI: 10.1007/s10682-022-10206-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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104
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Extended longevity of DNA preservation in Levantine Paleolithic sediments, Sefunim Cave, Israel. Sci Rep 2022; 12:14528. [PMID: 36008437 PMCID: PMC9411205 DOI: 10.1038/s41598-022-17399-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 07/25/2022] [Indexed: 11/09/2022] Open
Abstract
Paleogenomic research can elucidate the evolutionary history of human and faunal populations. Although the Levant is a key land-bridge between Africa and Eurasia, thus far, relatively little ancient DNA data has been generated from this region, since DNA degrades faster in warm climates. As sediments can be a source of ancient DNA, we analyzed 33 sediment samples from different sedimentological contexts in the Paleolithic layers of Sefunim Cave (Israel). Four contained traces of ancient Cervidae and Hyaenidae mitochondrial DNA. Dating by optical luminescence and radiocarbon indicates that the DNA comes from layers between 30,000 and 70,000 years old, surpassing theoretical expectations regarding the longevity of DNA deposited in such a warm environment. Both identified taxa are present in the zooarchaeological record of the site but have since gone extinct from the region, and a geoarchaeological study suggests little movement of the sediments after their deposition, lending further support to our findings. We provide details on the local conditions in the cave, which we hypothesize were particularly conducive to the long-term preservation of DNA-information that will be pertinent for future endeavors aimed at recovering ancient DNA from the Levant and other similarly challenging contexts.
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105
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Whole-genome resequencing of Chinese pangolins reveals a population structure and provides insights into their conservation. Commun Biol 2022; 5:821. [PMID: 36008681 PMCID: PMC9411537 DOI: 10.1038/s42003-022-03757-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 07/22/2022] [Indexed: 11/18/2022] Open
Abstract
Poaching and trafficking have a substantial negative impact on the population growth and range expansion of the Chinese pangolin (Manis pentadactyla). However, recently reported activities of Chinese pangolins in several sites of Guangdong province in China indicate a promising sign for the recovery of this threatened species. Here, we re-sequence genomes of 15 individuals and perform comprehensive population genomics analyses with previously published 22 individuals. These Chinese pangolins are found to be divided into three distinct populations. Multiple lines of evidence indicate the existence of a newly discovered population (CPA) comprises entirely of individuals from Guangdong province. The other two populations (CPB and CPC) have previously been documented. The genetic differentiation of the CPA and CPC is extremely large (FST = 0.541), which is larger than many subspecies-level differentiations. Even for the closer CPA and CPB, their differentiation (FST = 0.101) is still comparable with the population-level differentiation of many endangered species. Further analysis reveals that the CPA and CPB populations separate 2.5–4.0 thousand years ago (kya), and on the other hand, CPA and CPC diverge around 25–40 kya. The CPA population harbors more runs of homozygosity (ROHs) than the CPB and CPC populations, indicating that inbreeding is more prevalent in the CPA population. Although the CPC population has less mutational load than CPA and CPB populations, we predict that several Loss of Function (LoF) mutations will be translocated into the CPA or CPB populations by using the CPC as a donor population for genetic rescue. Our findings imply that the conservation of Chinese pangolins is challenging, and implementing genetic rescue among the three groups should be done with extreme caution. Whole-genome resequencing of Chinese pangolins reveals a new population CPA that is genetically distinct from and harbor more homozygosity than CPB and CPC populations, indicating prevalence in inbreeding and implying challenges in conservation.
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106
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Chavez DE, Gronau I, Hains T, Dikow RB, Frandsen PB, Figueiró HV, Garcez FS, Tchaicka L, de Paula RC, Rodrigues FHG, Jorge RSP, Lima ES, Songsasen N, Johnson WE, Eizirik E, Koepfli KP, Wayne RK. Comparative genomics uncovers the evolutionary history, demography, and molecular adaptations of South American canids. Proc Natl Acad Sci U S A 2022; 119:e2205986119. [PMID: 35969758 PMCID: PMC9407222 DOI: 10.1073/pnas.2205986119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/28/2022] [Indexed: 11/18/2022] Open
Abstract
The remarkable radiation of South American (SA) canids produced 10 extant species distributed across diverse habitats, including disparate forms such as the short-legged, hypercarnivorous bush dog and the long-legged, largely frugivorous maned wolf. Despite considerable research spanning nearly two centuries, many aspects of their evolutionary history remain unknown. Here, we analyzed 31 whole genomes encompassing all extant SA canid species to assess phylogenetic relationships, interspecific hybridization, historical demography, current genetic diversity, and the molecular bases of adaptations in the bush dog and maned wolf. We found that SA canids originated from a single ancestor that colonized South America 3.9 to 3.5 Mya, followed by diversification east of the Andes and then a single colonization event and radiation of Lycalopex species west of the Andes. We detected extensive historical gene flow between recently diverged lineages and observed distinct patterns of genomic diversity and demographic history in SA canids, likely induced by past climatic cycles compounded by human-induced population declines. Genome-wide scans of selection showed that disparate limb proportions in the bush dog and maned wolf may derive from mutations in genes regulating chondrocyte proliferation and enlargement. Further, frugivory in the maned wolf may have been enabled by variants in genes associated with energy intake from short-chain fatty acids. In contrast, unique genetic variants detected in the bush dog may underlie interdigital webbing and dental adaptations for hypercarnivory. Our analyses shed light on the evolution of a unique carnivoran radiation and how it was shaped by South American topography and climate change.
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Affiliation(s)
- Daniel E. Chavez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
- Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Reichman University, Herzliya 46150, Israel
| | - Taylor Hains
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637
| | - Rebecca B. Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560
| | - Paul B. Frandsen
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602
| | - Henrique V. Figueiró
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, 90619-900, Brazil
| | - Fabrício S. Garcez
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, 90619-900, Brazil
| | - Ligia Tchaicka
- Rede de Biodiversidade e Biotecnologia da Amazônia, Curso de Pós-Graduação em Recursos Aquáticos e Pesca, Universidade Estadual do Maranhão, São Luis, 2016-8100, Brazil
| | - Rogério C. de Paula
- Centro Nacional de Pesquisa e Conservação de Mamíferos Carnívoros, Instituto Chico Mendes de Conservação da Biodiversidade, 12952-011, Atibaia, Brazil
| | - Flávio H. G. Rodrigues
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Rodrigo S. P. Jorge
- Centro Nacional de Avaliação da Biodiversidade e de Pesquisa e Conservação do Cerrado, Instituto Chico Mendes de Conservação da Biodiversidade, Brasilia, 70670-350, Brazil
| | - Edson S. Lima
- Private address, Nova Xavantina, MT, 78690-000, Brazil
| | - Nucharin Songsasen
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
| | - Warren E. Johnson
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, 90619-900, Brazil
- Instituto Pró-Carnívoros, Atibaia, 12945-010, Brazil
- Instituto Nacional de Ciência e Tecnologia em Ecologia Evolução Conservação da Biodiverside, Universidade Federal de GoiásGoiânia, 74690-900, Brazil
| | - Klaus-Peter Koepfli
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
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107
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Újvári G, Klötzli U, Stevens T, Svensson A, Ludwig P, Vennemann T, Gier S, Horschinegg M, Palcsu L, Hippler D, Kovács J, Di Biagio C, Formenti P. Greenland Ice Core Record of Last Glacial Dust Sources and Atmospheric Circulation. JOURNAL OF GEOPHYSICAL RESEARCH. ATMOSPHERES : JGR 2022; 127:e2022JD036597. [PMID: 36245641 PMCID: PMC9542552 DOI: 10.1029/2022jd036597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 06/16/2023]
Abstract
Abrupt and large-scale climate changes have occurred repeatedly and within decades during the last glaciation. These events, where dramatic warming occurs over decades, are well represented in both Greenland ice core mineral dust and temperature records, suggesting a causal link. However, the feedbacks between atmospheric dust and climate change during these Dansgaard-Oeschger events are poorly known and the processes driving changes in atmospheric dust emission and transport remain elusive. Constraining dust provenance is key to resolving these gaps. Here, we present a multi-technique analysis of Greenland dust provenance using novel and established, source diagnostic isotopic tracers as well as results from a regional climate model including dust cycle simulations. We show that the existing dominant model for the provenance of Greenland dust as sourced from combined East Asian dust and Pacific volcanics is not supported. Rather, our clay mineralogical and Hf-Sr-Nd and D/H isotopic analyses from last glacial Greenland dust and an extensive range of Northern Hemisphere potential dust sources reveal three most likely scenarios (in order of probability): direct dust sourcing from the Taklimakan Desert in western China, direct sourcing from European glacial sources, or a mix of dust originating from Europe and North Africa. Furthermore, our regional climate modeling demonstrates the plausibility of European or mixed European/North African sources for the first time. We suggest that the origin of dust to Greenland is potentially more complex than previously recognized, demonstrating more uncertainty in our understanding dust climate feedbacks during abrupt events than previously understood.
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Affiliation(s)
- G. Újvári
- Centre for Astronomy and Earth SciencesInstitute for Geological and Geochemical ResearchEötvös Loránd Research NetworkBudapestHungary
- CSFKMTA Centre of ExcellenceBudapestHungary
- Department of Lithospheric ResearchUniversity of ViennaViennaAustria
| | - U. Klötzli
- Department of Lithospheric ResearchUniversity of ViennaViennaAustria
| | - T. Stevens
- Department of Earth SciencesUppsala UniversityUppsalaSweden
| | - A. Svensson
- Physics of Ice, Climate and EarthNiels Bohr InstituteUniversity of CopenhagenCopenhagenDenmark
| | - P. Ludwig
- Institute for Meteorology and Climate ResearchKarlsruhe Institute of TechnologyKarlsruheGermany
| | - T. Vennemann
- Institute of Earth Surface DynamicsUniversity of LausanneLausanneSwitzerland
| | - S. Gier
- Department of GeologyUniversity of ViennaViennaAustria
| | - M. Horschinegg
- Department of Lithospheric ResearchUniversity of ViennaViennaAustria
| | - L. Palcsu
- Isotope Climatology and Environmental Research CentreInstitute for Nuclear ResearchDebrecenHungary
| | - D. Hippler
- Institute of Applied GeosciencesGraz University of TechnologyGrazAustria
| | - J. Kovács
- Environmental Analytical and Geoanalytical Research GroupSzentágothai Research CentreUniversity of PécsPécsHungary
- Institute of Geography and Earth SciencesUniversity of PécsPécsHungary
| | - C. Di Biagio
- Université de Paris Cité and University Paris Est CreteilCNRSLISAParisFrance
| | - P. Formenti
- Université de Paris Cité and University Paris Est CreteilCNRSLISAParisFrance
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108
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Arekar K, Tiwari N, Sathyakumar S, Khaleel M, Karanth P. Geography vs. past climate: the drivers of population genetic structure of the Himalayan langur. BMC Ecol Evol 2022; 22:100. [PMID: 35971061 PMCID: PMC9377076 DOI: 10.1186/s12862-022-02054-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 08/03/2022] [Indexed: 11/24/2022] Open
Abstract
Background Contemporary species distribution, genetic diversity and evolutionary history in many taxa are shaped by both historical and current climate as well as topography. The Himalayas show a huge variation in topography and climatic conditions across its entire range, and have experienced major climatic fluctuations in the past. However, very little is known regarding how this heterogenous landscape has moulded the distribution of Himalayan fauna. A recent study examined the effect of these historical events on the genetic diversity of the Himalayan langurs in Nepal Himalaya. However, this study did not include the samples from the Indian Himalayan region (IHR). Therefore, here we revisit the questions addressed in the previous study with a near complete sampling from the IHR, along with the samples from the Nepal Himalaya. We used the mitochondrial Cytochrome-b (Cyt-b, 746 bp) region combined with multiple phylogeographic analyses and palaeodistribution modelling. Results Our dataset contained 144 sequences from the IHR as well as the Nepal Himalaya. Phylogenetic analysis showed a low divergent western clade nested within high divergent group of eastern lineages and in the network analysis we identified 22 haplotypes over the entire distribution range of the Himalayan langurs. Samples from the Nepal Himalaya showed geographically structured haplotypes corresponding to different river barriers, whereas samples from IHR showed star-like topology with no structure. Our statistical phylogeography analysis using diyABC supported the model of east to west colonisation of these langurs with founder event during colonisation. Analysis of demographic history showed that the effective population size of the Himalayan langurs decreased at the onset of last glacial maximum (LGM) and started increasing post LGM. The palaeodistribution modelling showed that the extent of suitable habitat shifted from low elevation central Nepal, and adjoining parts of north India, during LGM to the western Himalaya at present. Conclusion The current genetic diversity and distribution of Himalayan langurs in the Nepal Himalaya has been shaped by river barriers, whereas the rivers in the IHR had relatively less time to act as a strong genetic barrier after the recent colonisation event. Further, the post LGM expansion could have had confounding effect on Himalayan langur population structure in both Nepal Himalaya and IHR. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02054-1.
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109
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Malan A, von der Heyden S, Herron S, Arnould JPY, Kirkwood R, Matthee CA. Palaeoclimatic changes resulted in range expansion and subsequent divergence in brown fur seals, Arctocephalus pusillus. Biol Lett 2022; 18:20220285. [PMID: 36043305 PMCID: PMC9428522 DOI: 10.1098/rsbl.2022.0285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/11/2022] [Indexed: 11/12/2022] Open
Abstract
Past climatic change as a driving force of marine diversification is still largely unclear, particularly for Southern Hemisphere species. Here, we present a case using the brown fur seal, Arctocephalus pusillus, assessing the geographical structure and demographic history using mitochondrial and nuclear data. Results show the two previously defined subspecies (one from Australia and the other from southern Africa) are phylogeographically distinct. Migration analyses based on nuclear data suggest the absence of migrants among the two genetically close assemblages. The demographic history of A. pusillus is characterized by a glacial population expansion (approx. 18 kya) in the southern African lineage, which coincides with time estimates of population expansion of prey species of seals. Approximate Bayesian calculations support an eastward dispersal event during the Last Glacial Maximum when sea levels were lower, followed by a postglacial divergence event, approximately 13 kya. The demographic history of the brown fur seal in the Southern Oceans provides support that recent palaeoclimatic changes could have facilitated expansions in some marine species and that postglacial sea-level rise may have acted as a dispersal barrier for species mostly confined to continental shelves.
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Affiliation(s)
- A. Malan
- Department Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - S. von der Heyden
- Department Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - S. Herron
- Department Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - J. P. Y. Arnould
- School of Life and Environmental Sciences, Deakin University, Burwood, Victoria, Australia
| | - R. Kirkwood
- South Australian Research and Development Institute, Aquatic Sciences, West Beach, South Australia 5024, Australia
- Research Department, Phillip Island Nature Parks, Cowes, Victoria 3922, Australia
| | - C. A. Matthee
- Department Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
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110
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Demographic Expansions and the Emergence of Host Specialization in Genetically Distinct Ecotypes of the Tick-Transmitted Bacterium Anaplasma phagocytophilum. Appl Environ Microbiol 2022; 88:e0061722. [PMID: 35867580 PMCID: PMC9317897 DOI: 10.1128/aem.00617-22] [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: 01/13/2023] Open
Abstract
In Europe, genetically distinct ecotypes of the tick-vectored bacterium Anaplasma phagocytophilum circulate among mammals in three discrete enzootic cycles. To date, potential ecological factors that contributed to the emergence of these divergent ecotypes have been poorly studied. Here, we show that the ecotype that predominantly infects roe deer (Capreolus capreolus) is evolutionarily derived. Its divergence from a host generalist ancestor occurred after the last glacial maximum as mammal populations, including roe deer, recolonized the European mainland from southern refugia. We also provide evidence that this host specialist ecotype's effective population size (Ne) has tracked changes in the population of its roe deer host. Specifically, both host and bacterium have undergone substantial increases in Ne over the past 1,500 years. In contrast, we show that while it appears to have undergone a major population expansion starting ~3,500 years ago, in the past 500 years, the contemporary host generalist ecotype has experienced a substantial reduction in genetic diversity levels, possibly as a result of reduced opportunities for transmission between competent hosts. IMPORTANCE The findings of this study reveal specific events important for the evolution of host specialization in a naturally occurring, obligately intracellular bacterial pathogen. Specifically, they show that host range shifts and the emergence of host specialization may occur during periods of population growth in a generalist ancestor. Our results also demonstrate the close correlation between demographic patterns in host and pathogen for a specialist system. These findings have important relevance for understanding the evolution of host range diversity. They may inform future work on host range dynamics, and they provide insights for understanding the emergence of pathogens that have human and veterinary health implications.
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111
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Tiley GP, van Elst T, Teixeira H, Schüßler D, Salmona J, Blanco MB, Ralison JM, Randrianambinina B, Rasoloarison RM, Stahlke AR, Hohenlohe PA, Chikhi L, Louis EE, Radespiel U, Yoder AD. Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests. Mol Ecol 2022; 31:4901-4918. [PMID: 35880414 DOI: 10.1111/mec.16632] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 06/25/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
Madagascar's Central Highlands are largely composed of grasslands, interspersed with patches of forest. The historical perspective was that Madagascar's grasslands had anthropogenic origins, but emerging evidence suggests that grasslands were a component of the pre-human Central Highlands vegetation. Consequently, there is now vigorous debate regarding the extent to which these grasslands have expanded due to anthropogenic pressures. Here, we shed light on the temporal dynamics of Madagascar's vegetative composition by conducting a population genomic investigation of Goodman's mouse lemur (Microcebus lehilahytsara; Cheirogaleidae). These small-bodied primates occur both in Madagascar's eastern rainforests and in the Central Highlands, making them a valuable indicator species. Population divergences among forest-dwelling mammals will reflect changes to their habitat, including fragmentation, whereas patterns of post-divergence gene flow can reveal formerly wooded migration corridors. To explore these patterns, we used RADseq data to infer population genetic structure, demographic models of post-divergence gene flow, and population size change through time. The results offer evidence that open habitats are an ancient component of the Central Highlands, and that wide-spread forest fragmentation occurred naturally during a period of decreased precipitation near the Last Glacial Maximum. Models of gene flow suggest that migration across the Central Highlands has been possible from the Pleistocene through the recent Holocene via riparian corridors. Though our findings support the hypothesis that Central Highland grasslands predate human arrival, we also find evidence for human-mediated population declines. This highlights the extent to which species imminently threatened by human-mediated deforestation may already be vulnerable from paleoclimatic conditions.
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Affiliation(s)
- George P Tiley
- Department of Biology, Duke University, Durham, NC, USA.,Royal Botanic Gardens Kew, Richmond, UK
| | - Tobias van Elst
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Helena Teixeira
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Dominik Schüßler
- Research Group Vegetation Ecology and Nature Conservation, Institute of Biology and Chemistry, University of Hildesheim, Hildesheim, Germany
| | - Jordi Salmona
- CNRS, Université Paul Sabatier, IRD; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
| | | | - José M Ralison
- Département de Biologie Animale, Université d'Antananarivo, Antananarivo, Madagascar
| | - Blanchard Randrianambinina
- Group d'Etude et de Recherche sur les Primates de Madagascar (GERP), Antananarivo, Madagascar.,Faculté des Sciences, University of Mahajanga, Mahajanga, Madagascar
| | - Rodin M Rasoloarison
- Département de Biologie Animale, Université d'Antananarivo, Antananarivo, Madagascar.,Group d'Etude et de Recherche sur les Primates de Madagascar (GERP), Antananarivo, Madagascar
| | - Amanda R Stahlke
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Lounès Chikhi
- CNRS, Université Paul Sabatier, IRD; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France.,Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras, Portugal
| | - Edward E Louis
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA
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112
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Zhang X, Ji X, Li C, Yang T, Huang J, Zhao Y, Wu Y, Ma S, Pang Y, Huang Y, He Y, Su B. A Late Pleistocene human genome from Southwest China. Curr Biol 2022; 32:3095-3109.e5. [PMID: 35839766 DOI: 10.1016/j.cub.2022.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 05/27/2022] [Accepted: 06/08/2022] [Indexed: 11/25/2022]
Abstract
Southern East Asia is the dispersal center regarding the prehistoric settlement and migrations of modern humans in Asia-Pacific regions. However, the settlement pattern and population structure of paleolithic humans in this region remain elusive, and ancient DNA can provide direct information. Here, we sequenced the genome of a Late Pleistocene hominin (MZR), dated ∼14.0 thousand years ago from Red Deer Cave located in Southwest China, which was previously reported possessing mosaic features of modern and archaic hominins. MZR is the first Late Pleistocene genome from southern East Asia. Our results indicate that MZR is a modern human who represents an early diversified lineage in East Asia. The mtDNA of MZR belongs to an extinct basal lineage of the M9 haplogroup, reflecting a rich matrilineal diversity in southern East Asia during the Late Pleistocene. Combined with the published data, we detected clear genetic stratification in ancient southern populations of East/Southeast Asia and some degree of south-versus-north divergency during the Late Pleistocene, and MZR was identified as a southern East Asian who exhibits genetic continuity to present day populations. Markedly, MZR is linked deeply to the East Asian ancestry that contributed to First Americans.
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Affiliation(s)
- Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
| | - Xueping Ji
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Department of Paleoanthropology, Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China.
| | - Chunmei Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
| | - Tingyu Yang
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| | - Jiahui Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yinhui Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Wu
- Department of Paleoanthropology, Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China; School of History, Wuhan University, Wuhan 430072, China; Archaeological Institute for Yangtze Civilization, Wuhan University, Wuhan 430072, China
| | - Shiwu Ma
- Mengzi Institute of Cultural Relics, Mengzi, Yunnan Province 661100, China
| | - Yuhong Pang
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| | - Yanyi Huang
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China.
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113
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Plis K, Niedziałkowska M, Borowik T, Lang J, Heddergott M, Tiainen J, Bunevich A, Šprem N, Paule L, Danilkin A, Kholodova M, Zvychaynaya E, Kashinina N, Pokorny B, Flajšman K, Paulauskas A, Djan M, Ristić Z, Novák L, Kusza S, Miller C, Tsaparis D, Stoyanov S, Shkvyria M, Suchentrunk F, Kutal M, Lavadinović V, Šnjegota D, Krapal AM, Dănilă G, Veeroja R, Dulko E, Jędrzejewska B. Mitochondrial DNA diversity and the population genetic structure of contemporary roe deer (Capreolus capreolus) in Europe. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00274-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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114
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Pacheco C, Stronen AV, Jędrzejewska B, Plis K, Okhlopkov IM, Mamaev NV, Drovetski SV, Godinho R. Demography and evolutionary history of grey wolf populations around the Bering Strait. Mol Ecol 2022; 31:4851-4865. [PMID: 35822863 PMCID: PMC9545117 DOI: 10.1111/mec.16613] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 06/16/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
Glacial and interglacial periods throughout the Pleistocene have been substantial drivers of change in species distributions. Earlier analyses suggested that modern grey wolves (Canis lupus) trace their origin to a single Late Pleistocene Beringian population that expanded east and westwards, starting c. 25,000 years ago (ya). Here, we examined the demographic and phylogeographic histories of extant populations around the Bering Strait with wolves from two inland regions of the Russian Far East (RFE) and one coastal and two inland regions of North‐western North America (NNA), genotyped for 91,327 single nucleotide polymorphisms. Our results indicated that RFE and NNA wolves had a common ancestry until c. 34,400 ya, suggesting that these populations started to diverge before the previously proposed expansion out of Beringia. Coastal and inland NNA populations diverged c. 16,000 ya, concordant with the minimum proposed date for the ecological viability of the migration route along the Pacific Northwest coast. Demographic reconstructions for inland RFE and NNA populations reveal spatial and temporal synchrony, with large historical effective population sizes that declined throughout the Pleistocene, possibly reflecting the influence of broadscale climatic changes across continents. In contrast, coastal NNA wolves displayed a consistently lower effective population size than the inland populations. Differences between the demographic history of inland and coastal wolves may have been driven by multiple ecological factors, including historical gene flow patterns, natural landscape fragmentation, and more recent anthropogenic disturbance.
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Affiliation(s)
- Carolina Pacheco
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Astrid Vik Stronen
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,Department of Biotechnology and Life Sciences, Insubria University, Varese, Italy.,Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Kamila Plis
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Innokentiy M Okhlopkov
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Nikolay V Mamaev
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Sergei V Drovetski
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
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115
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Huang X, Xia ZY, Bin X, He G, Guo J, Adnan A, Yin L, Huang Y, Zhao J, Yang Y, Ma F, Li Y, Hu R, Yang T, Wei LH, Wang CC. Genomic Insights Into the Demographic History of the Southern Chinese. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.853391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Southern China is the birthplace of rice-cultivating agriculture and different language families and has also witnessed various human migrations that facilitated cultural diffusions. The fine-scale demographic history in situ that forms present-day local populations, however, remains unclear. To comprehensively cover the genetic diversity in East and Southeast Asia, we generated genome-wide SNP data from 211 present-day Southern Chinese and co-analyzed them with ∼1,200 ancient and modern genomes. In Southern China, language classification is significantly associated with genetic variation but with a different extent of predictability, and there is strong evidence for recent shared genetic history particularly in Hmong–Mien and Austronesian speakers. A geography-related genetic sub-structure that represents the major genetic variation in Southern East Asians is established pre-Holocene and its extremes are represented by Neolithic Fujianese and First Farmers in Mainland Southeast Asia. This sub-structure is largely reduced by admixture in ancient Southern Chinese since > ∼2,000 BP, which forms a “Southern Chinese Cluster” with a high level of genetic homogeneity. Further admixture characterizes the demographic history of the majority of Hmong–Mien speakers and some Kra-Dai speakers in Southwest China happened ∼1,500–1,000 BP, coeval to the reigns of local chiefdoms. In Yellow River Basin, we identify a connection of local populations to genetic sub-structure in Southern China with geographical correspondence appearing > ∼9,000 BP, while the gene flow likely closely related to “Southern Chinese Cluster” since the Longshan period (∼5,000–4,000 BP) forms ancestry profile of Han Chinese Cline.
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116
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Reply to: "Steller's sea cow uncertain history illustrates importance of ecological context when interpreting demographic histories from genomes". Nat Commun 2022; 13:3672. [PMID: 35764648 PMCID: PMC9240042 DOI: 10.1038/s41467-022-31382-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 06/14/2022] [Indexed: 11/15/2022] Open
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117
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Birds adapted to cold conditions show greater changes in range size related to past climatic oscillations than temperate birds. Sci Rep 2022; 12:10813. [PMID: 35752649 PMCID: PMC9233688 DOI: 10.1038/s41598-022-14972-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
Investigation of ecological responses of species to past climate oscillations provides crucial information to understand the effects of global warming. In this work, we investigated how past climate changes affected the distribution of six bird species with different climatic requirements and migratory behaviours in the Western Palearctic and in Africa. Species Distribution Models and Marine Isotopic Stage (MIS) 2 fossil occurrences of selected species were employed to evaluate the relation between changes in range size and species climatic tolerances. The Last Glacial Maximum (LGM) range predictions, generally well supported by the MIS 2 fossil occurrences, suggest that cold-dwelling species considerably expanded their distribution in the LGM, experiencing more pronounced net changes in range size compared to temperate species. Overall, the thermal niche proves to be a key ecological trait for explaining the impact of climate change in species distributions. Thermal niche is linked to range size variations due to climatic oscillations, with cold-adapted species currently suffering a more striking range reduction compared to temperate species. This work also supports the persistence of Afro-Palearctic migrations during the LGM due to the presence of climatically suitable wintering areas in Africa even during glacial maxima.
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118
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Stojak J, Jędrzejewska B. Extinction and replacement events shaped the historical biogeography of Arctic mammals in Europe: new models of species response. Mamm Rev 2022. [DOI: 10.1111/mam.12298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joanna Stojak
- Mammal Research Institute, Polish Academy of Sciences ul. Stoczek 1, 17‐230 Białowieża Poland
- Department of Ecology and Evolutionary Biology, Paleogenomics Laboratory University of California Santa Cruz Santa Cruz CA 95064 USA
| | - Bogumiła Jędrzejewska
- Mammal Research Institute, Polish Academy of Sciences ul. Stoczek 1, 17‐230 Białowieża Poland
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119
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Wang L, Sun X, Peng Y, Chen K, Wu S, Guo Y, Zhang J, Yang H, Jin T, Wu L, Zhou X, Liang B, Zhao Z, Liu D, Fei Z, Bai L. Genomic insights into the origin, adaptive evolution, and herbicide resistance of Leptochloa chinensis, a devastating tetraploid weedy grass in rice fields. MOLECULAR PLANT 2022; 15:1045-1058. [PMID: 35524410 DOI: 10.1016/j.molp.2022.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 04/30/2022] [Accepted: 05/01/2022] [Indexed: 06/14/2023]
Abstract
Chinese sprangletop (Leptochloa chinensis), belonging to the grass subfamily Chloridoideae, is one of the most notorious weeds in rice ecosystems. Here, we report a chromosome-scale reference genome assembly and a genomic variation map of the tetraploid L. chinensis. The L. chinensis genome is derived from two diploid progenitors that diverged ∼10.9 million years ago, and its two subgenomes display neither fractionation bias nor overall gene expression dominance. Comparative genomic analyses reveal substantial genome rearrangements in L. chinensis after its divergence from the common ancestor of Chloridoideae and, together with transcriptome profiling, demonstrate the important contribution of tetraploidization to the gene sources for the herbicide resistance of L. chinensis. Population genomic analyses of 89 accessions from China reveal that L. chinensis accessions collected from southern/southwestern provinces have substantially higher nucleotide diversity than those from the middle and lower reaches of the Yangtze River, suggesting that L. chinensis spread in China from the southern/southwestern provinces to the middle and lower reaches of the Yangtze River. During this spread, L. chinensis developed significantly increased herbicide resistance, accompanied by the selection of numerous genes involved in herbicide resistance. Taken together, our study generated valuable genomic resources for future fundamental research and agricultural management of L. chinensis, and provides significant new insights into the herbicide resistance as well as the origin and adaptive evolution of L. chinensis.
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Affiliation(s)
- Lifeng Wang
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Xuepeng Sun
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA; College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
| | - Yajun Peng
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ke Chen
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Shan Wu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yanan Guo
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jingyuan Zhang
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao 266000, China
| | - Haona Yang
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Tao Jin
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao 266000, China
| | - Lamei Wu
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Xiaomao Zhou
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Bin Liang
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Zhenghong Zhao
- Hunan Weed Science Key Laboratory, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ducai Liu
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA; USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA.
| | - Lianyang Bai
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
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120
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Hatton A, Collins B, Schoville BJ, Wilkins J. Ostrich eggshell beads from Ga-Mohana Hill North Rockshelter, southern Kalahari, and the implications for understanding social networks during Marine Isotope Stage 2. PLoS One 2022; 17:e0268943. [PMID: 35648787 PMCID: PMC9159631 DOI: 10.1371/journal.pone.0268943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 05/11/2022] [Indexed: 11/23/2022] Open
Abstract
Ostrich eggshell (OES) beads from southern African archaeological contexts shed light on past traditions of personal ornamentation, and they are also argued to provide a proxy for understanding past social networks. However, OES beads are often understudied and not reported on in detail. In particular, there has been little research on OES bead variation during Marine Isotope Stage 2 (29,000–12,000 years ago) which includes the Last Glacial Maximum when changing climatic conditions are hypothesized to have significant impact on forager social networks. Here, we present the first technological analysis of terminal Pleistocene OES beads and fragments in the Kalahari from the ~15 ka levels at Ga-Mohana Hill North Rockshelter. We contextualise these findings through comparison with coeval OES bead assemblages across southern Africa during MIS 2. Results indicate that OES beads were manufactured at Ga-Mohana Hill North during the terminal Pleistocene occupation, based on the presence of most stages of bead manufacture. The review shows that OES beads were present across southern Africa through MIS 2, suggesting that culturing of the body was an embodied and persistent practice during that time. While the importance of OES beads as decorative objects was shared by populations across southern Africa, variation in bead diameters indicate that there was stylistic variation.
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Affiliation(s)
- Amy Hatton
- Extreme Events Research Group, Max Planck Institutes for Science of Human History, Chemical Ecology and Biogeochemistry, Jena, Germany
- Department of Archaeology, Max Planck Institute for Science of Human History, Jena, Germany
- Department of Archaeology, University of Cape Town, Human Evolution Research Institute, Cape Town, Private Bag, Rondebosch, South Africa
- * E-mail:
| | - Benjamin Collins
- Department of Archaeology, University of Cape Town, Human Evolution Research Institute, Cape Town, Private Bag, Rondebosch, South Africa
- Department of Anthropology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Benjamin J. Schoville
- Department of Archaeology, University of Cape Town, Human Evolution Research Institute, Cape Town, Private Bag, Rondebosch, South Africa
- School of Social Science, University of Queensland, St Lucia, Queensland, Australia
| | - Jayne Wilkins
- Department of Archaeology, University of Cape Town, Human Evolution Research Institute, Cape Town, Private Bag, Rondebosch, South Africa
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia
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121
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The genomic origins of the world's first farmers. Cell 2022; 185:1842-1859.e18. [PMID: 35561686 PMCID: PMC9166250 DOI: 10.1016/j.cell.2022.04.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/04/2022] [Accepted: 04/06/2022] [Indexed: 11/24/2022]
Abstract
The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness. This modeling elucidates the demographic processes at the root of the Neolithic transition and leads to a spatial interpretation of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene.
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122
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Richards EJ, Martin CH. We get by with a little help from our friends: shared adaptive variation provides a bridge to novel ecological specialists during adaptive radiation. Proc Biol Sci 2022; 289:20220613. [PMID: 35611537 PMCID: PMC9130792 DOI: 10.1098/rspb.2022.0613] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Adaptive radiations involve astounding bursts of phenotypic, ecological and species diversity. However, the microevolutionary processes that underlie the origins of these bursts are still poorly understood. We report the discovery of an intermediate C. sp. ‘wide-mouth’ scale-eating ecomorph in a sympatric radiation of Cyprinodon pupfishes, illuminating the transition from a widespread algae-eating generalist to a novel microendemic scale-eating specialist. We first show that this ecomorph occurs in sympatry with generalist C. variegatus and scale-eating specialist C. desquamator on San Salvador Island, Bahamas, but is genetically differentiated, morphologically distinct and often consumes scales. We then compared the timing of selective sweeps on shared and unique adaptive variants in trophic specialists to characterize their adaptive walk. Shared adaptive regions swept first in both the specialist desquamator and the intermediate ‘wide-mouth’ ecomorph, followed by unique sweeps of introgressed variation in ‘wide-mouth’ and de novo variation in desquamator. The two scale-eating populations additionally shared 9% of their hard selective sweeps with the molluscivore C. brontotheroides, despite no single common ancestor among specialists. Our work provides a new microevolutionary framework for investigating how major ecological transitions occur and illustrates how both shared and unique genetic variation can provide a bridge for multiple species to access novel ecological niches.
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Affiliation(s)
- Emilie J Richards
- Department of Integrative Biology, University of California, Berkeley, CA, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Christopher H Martin
- Department of Integrative Biology, University of California, Berkeley, CA, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
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123
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Maltseva AL, Lobov AA, Pavlova PA, Panova M, Gafarova ER, Marques JP, Danilov LG, Granovitch AI. Orphan gene in Littorina: An unexpected role of symbionts in the host evolution. Gene 2022; 824:146389. [PMID: 35257790 DOI: 10.1016/j.gene.2022.146389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/29/2022] [Accepted: 02/28/2022] [Indexed: 11/16/2022]
Abstract
Mechanisms of reproductive isolation between closely related sympatric species are of high evolutionary significance as they may function as initial drivers of speciation and protect species integrity afterwards. Proteins involved in the establishment of reproductive barriers often evolve fast and may be key players in cessation of gene flow between the incipient species. The five Atlantic Littorina (Neritrema) species represent a notable example of recent radiation. The geographic ranges of these young species largely overlap and the mechanisms of reproductive isolation are poorly understood. In this study, we performed a detailed analysis of the reproductive protein LOSP, previously identified in Littorina. We showed that this protein is evolutionary young and taxonomically restricted to the genus Littorina. It has high sequence variation both within and between Littorina species, which is compatible with its presumable role in the reproductive isolation. The strongest differences in the LOSP structure were detected between Littorina subgenera with distinctive repetitive motifs present exclusively in the Neritrema species, but not in L. littorea. Moreover, the sequence of these repetitive structural elements demonstrates a high homology with genetic elements of bacteria, identified as components of Littorina associated microbiomes. We suggest that these elements were acquired from a symbiotic bacterial donor via horizontal genetic transfer (HGT), which is indirectly confirmed by the presence of multiple transposable elements in the LOSP flanking and intronic regions. Furthermore, we hypothesize that this HGT-driven evolutionary innovation promoted LOSP function in reproductive isolation, which might be one of the factors determining the intensive cladogenesis in the Littorina (Neritrema) lineage in contrast to the anagenesis in the L. littorea clade.
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Affiliation(s)
- A L Maltseva
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia.
| | - A A Lobov
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia; Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Sciences, St Petersburg, Russia
| | - P A Pavlova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - M Panova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia; Department of Marine Sciences - Tjärnö, University of Gothenburg, Sweden
| | - E R Gafarova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - J P Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências do Porto, 4169-007 Porto, Portugal; ISEM, Univ Montpellier, CNRS, EPHE, IRD, 34095 Montpellier, France
| | - L G Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - A I Granovitch
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
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124
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Cai D, Zhu S, Gong M, Zhang N, Wen J, Liang Q, Sun W, Shao X, Guo Y, Cai Y, Zheng Z, Zhang W, Hu S, Wang X, Tian H, Li Y, Liu W, Yang M, Yang J, Wu D, Orlando L, Jiang Y. Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene. eLife 2022; 11:73346. [PMID: 35543411 PMCID: PMC9142152 DOI: 10.7554/elife.73346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
The exceptionally rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses, and zebras represent three extant subgenera of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 archaeological specimens from Northern China in the Holocene that could be assigned morphologically and genetically to Equus ovodovi, a species representative of Sussemionus. We present the first high-quality complete genome of the Sussemionus lineage, which was sequenced to 13.4× depth of coverage. Radiocarbon dating demonstrates that this lineage survived until ~3500 years ago, despite continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree and found that Sussemionus diverged from the ancestor of non-caballine equids ~2.3–2.7 million years ago and possibly remained affected by secondary gene flow post-divergence. We found that the small genetic diversity, rather than enhanced inbreeding, limited the species’ chances of survival. Our work adds to the growing literature illustrating how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.
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Affiliation(s)
- Dawei Cai
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Siqi Zhu
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Mian Gong
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Naifan Zhang
- Bioarchaeology Laboratory, Jilin University, Changchuin, China
| | - Jia Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qiyao Liang
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Weilu Sun
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Xinyue Shao
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Yaqi Guo
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Yudong Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhuqing Zheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wei Zhang
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Songmei Hu
- Shaanxi Provincial Institute of Archaeology, Xi'an, China
| | - Xiaoyang Wang
- Ningxia Institute of Cultural Relics and Archaeology, Yinchuan, China
| | - He Tian
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Youqian Li
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Wei Liu
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Miaomiao Yang
- Shaanxi Provincial Institute of Archaeology, Xi'an, China
| | - Jian Yang
- Ningxia Institute of Cultural Relics and Archaeology, Yinchuan, China
| | - Duo Wu
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Ludovic Orlando
- 7Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, CNRS UMR 5288, Toulouse, France
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Deeply divergent freshwater fish species within a single river system in central Sulawesi. Mol Phylogenet Evol 2022; 173:107519. [DOI: 10.1016/j.ympev.2022.107519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 01/02/2023]
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Draft Genome Assembly of an Iconic Arctic Species: Muskox (Ovibos moschatus). Genes (Basel) 2022; 13:genes13050809. [PMID: 35627194 PMCID: PMC9140810 DOI: 10.3390/genes13050809] [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: 04/15/2022] [Revised: 04/25/2022] [Accepted: 04/29/2022] [Indexed: 02/01/2023] Open
Abstract
Muskoxen (Ovibos moschatus) are Arctic species within the Caprinae subfamily that are economically and culturally significant to northern Indigenous communities. Low genetic diversity from repeated genetic bottlenecks, coupled with the effects of Arctic warming (e.g., heat stress, changing forage, pathogen range expansions), present conservation concerns for this species. Reference genome assemblies enhance our ecological and evolutionary understanding of species (which in turn aid conservation efforts). Herein, we provide a full draft reference genome of muskox using Illumina Hiseq data and cross-species scaffolding. The final reference assembly yielded a genome of 2,621,890,883 bp in length, a scaffold N50 of ~13.2 million, and an annotation identifying ~19.3 k genes. The muskox genome assembly and annotation were then used to reconstruct a phylogenetic tree which estimated muskoxen diverged from other ungulate species~12 Mya. To gain insight into the demographic history of muskoxen we also performed pairwise sequentially Markovian coalescent (PSMC) that identified two population bottlenecks coinciding with major glaciation events contributing to the notoriously low genetic variation observed in muskoxen. Overall, this genome assembly provides a foundation for future population genomic studies, such as latitudinal analyses, to explore the capacity of muskoxen to adapt to rapidly changing environments.
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Boyette AH, Lew-Levy S, Jang H, Kandza V. Social ties in the Congo Basin: insights into tropical forest adaptation from BaYaka and their neighbours. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200490. [PMID: 35249385 PMCID: PMC8899623 DOI: 10.1098/rstb.2020.0490] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 01/05/2022] [Indexed: 12/18/2022] Open
Abstract
Investigating past and present human adaptation to the Congo Basin tropical forest can shed light on how climate and ecosystem variability have shaped human evolution. Here, we first review and synthesize genetic, palaeoclimatological, linguistic and historical data on the peopling of the Congo Basin. While forest fragmentation led to the increased genetic and geographical divergence of forest foragers, these groups maintained long-distance connectivity. The eventual expansion of Bantu speakers into the Congo Basin provided new opportunities for forging inter-group links, as evidenced by linguistic shifts and historical accounts. Building from our ethnographic work in the northern Republic of the Congo, we show how these inter-group links between forest forager communities as well as trade relationships with neighbouring farmers facilitate adaptation to ecoregions through knowledge exchange. While researchers tend to emphasize forager-farmer interactions that began in the Iron Age, we argue that foragers' cultivation of relational wealth with groups across the region played a major role in the initial occupation of the Congo Basin and, consequently, in cultural evolution among the ancestors of contemporary peoples. This article is part of the theme issue 'Tropical forests in the deep human past'.
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Affiliation(s)
- Adam H. Boyette
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Sheina Lew-Levy
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Department of Comparative Cultural Psychology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Haneul Jang
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Vidrige Kandza
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
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128
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Su T, He B, Zhao F, Jiang K, Lin G, Huang Z. Population genomics and phylogeography of
Colletes gigas
, a wild bee specialized on winter flowering plants. Ecol Evol 2022; 12:e8863. [PMID: 35494503 PMCID: PMC9035574 DOI: 10.1002/ece3.8863] [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: 03/30/2022] [Accepted: 04/05/2022] [Indexed: 11/09/2022] Open
Abstract
Diet specialization may affect the population genetic structure of pollinators by reducing gene flow and driving genetic differentiation, especially in pollen‐specialist bees. Colletes gigas is a pollen‐specialist pollinator of Camellia oleifera, one of the most important staple oil crops in China. Ca. oleifera blooms in cold climates and contains special compounds that make it an unusable pollen source to other pollinators. Thus, C. gigas undoubtedly plays a key role as the main pollinator of Ca. oleifera, with biological and economic significance. Here, we use a population genomic approach to analyze the roles of geography and climate on the genetic structure, genetic diversity, and demographic history of C. gigas. A total of 1,035,407 SNPs were identified from a 582.77 Gb dataset. Clustering and phylogenetic analyses revealed a marked genetic structure, with individuals grouped into nine local clusters. A significant isolation by distance was detected by both the Mantel test (R = .866, p = .008) and linear regression (R2 = .616, p < .001). Precipitation and sunshine duration were positively and significantly (R ≥ .765, p ≤ .016) correlated with observed heterozygosity (Ho) and expected heterozygosity (He). These results showed that C. gigas populations had a distinct phylogeographic pattern determined by geographical distance and environmental factors (precipitation and sunshine duration). In addition, an analysis of paleogeographic dynamics indicated that C. gigas populations exhibited patterns of glacial expansion and interglacial contraction, likely resulting from post‐glacial habitat contraction and fragmentation. Our results indicated that the peculiar phylogeographic patterns in C. gigas populations may be related to their specialization under long‐term adaptation to host plants. This work improves our understanding of the population genetics in pollen‐specialist bees. The distinct genetic clusters identified in this study should be taken into consideration for the protection and utilization of this specialized crop pollinator.
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Affiliation(s)
- Tianjuan Su
- School of Life Sciences Jinggangshan University Ji'an China
| | - Bo He
- School of Life Sciences Jinggangshan University Ji'an China
- College of Life Sciences Anhui Normal University Wuhu China
| | - Fang Zhao
- School of Life Sciences Jinggangshan University Ji'an China
| | - Kai Jiang
- School of Life Sciences Jinggangshan University Ji'an China
| | - Gonghua Lin
- School of Life Sciences Jinggangshan University Ji'an China
| | - Zuhao Huang
- School of Life Sciences Jinggangshan University Ji'an China
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Late-Glacial and Holocene Lake-Level Fluctuations on the Kenai Lowland, Reconstructed from Satellite-Fen Peat Deposits and Ice-Shoved Ramparts, Kenai Peninsula, Alaska. QUATERNARY 2022. [DOI: 10.3390/quat5020023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Recent decades of warmer climate have brought drying wetlands and falling lake levels to southern Alaska. These recent changes can be placed into a longer-term context of postglacial lake-level fluctuations that include low stands that were as much as 7 m lower than present at eight lakes on the Kenai Lowland. Closed-basin lakes on the Kenai Lowland are typically ringed with old shorelines, usually as wave-cut scarps, cut several meters above modern lake levels; the scarps formed during deglaciation at 25–19 ka in a kettle moraine topography on the western Kenai Lowland. These high-water stands were followed by millennia of low stands, when closed-basin lake levels were drawn down by 5–10 m or more. Peat cores from satellite fens near or adjoining the eight closed-basin lakes show that a regional lake level rise was underway by at least 13.4 ka. At Jigsaw Lake, a detailed study of 23 pairs of overlapping sediment cores, seismic profiling, macrofossil analysis, and 58 AMS radiocarbon dates reveal rapidly rising water levels at 9–8 ka that caused large slabs of peat to slough off and sink to the lake bottom. These slabs preserve an archive of vegetation that had accumulated on a lakeshore apron exposed during the preceding drawdown period. They also preserve evidence of a brief period of lake level rise at 4.7–4.5 ka. We examined plant succession using in situ peat sequences in nine satellite fens around Jigsaw Lake that indicated increased effective moisture between 4.6 and 2.5 ka synchronous with the lake level rise. Mid- to late-Holocene lake high stands in this area are recorded by numerous ice-shoved ramparts (ISRs) along the shores. ISRs at 15 lakes show that individual ramparts typically record several shove events, separated by hundreds or thousands of years. Most ISRs date to within the last 5200 years and it is likely that older ISRs were erased by rising lake levels during the mid- to late Holocene. This study illustrates how data on vegetation changes in hydrologically coupled satellite-fen peat records can be used to constrain the water level histories in larger adjacent lakes. We suggest that this method could be more widely utilized for paleo-lake level reconstruction.
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Liu H, Jiang F, Wang S, Wang H, Wang A, Zhao H, Xu D, Yang B, Fan W. Chromosome-level genome of the globe skimmer dragonfly (Pantala flavescens). Gigascience 2022; 11:6563153. [PMID: 35373834 PMCID: PMC8978299 DOI: 10.1093/gigascience/giac009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/24/2021] [Accepted: 01/19/2022] [Indexed: 11/29/2022] Open
Abstract
Background The globe skimmer dragonfly (Pantala flavescens) is a notable Odonata insect distributed in nature fields and farmlands worldwide, and it is commonly recognized as a natural enemy because it preys on agricultural pests and health pests. As one of the sister groups of winged insects, odonatan species are key to understanding the evolution of insect wings. Findings We present a high-quality reference genome of P. flavescens, which is the first chromosome-level genome in the Palaeoptera (Odonata and Ephemeroptera). The assembled genome size was 662 Mb, with a contig N50 of 16.2 Mb. Via Hi-C scaffolding, 648 Mb (97.9%) of contig sequences were clustered, ordered, and assembled into 12 large scaffolds, each corresponding to a natural chromosome. The X chromosome was identified by sequence coverage depth. The repetitive sequences and gene density of the X chromosome are similar to those of autosomal sequences, but the X chromosome shows a much lower degree of heterozygosity. Our analysis shows that the effective population size experienced 3 declining events, which may have been caused by climate change and environmental pollution. Conclusions The genome of P. flavescens provides more information on the biology and evolution of insects and will help for the use of this species in pest control.
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Affiliation(s)
- Hangwei Liu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Sen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Hanbo Zhao
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Dong Xu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Boyuan Yang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
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Wang Z, Pierce NE. Fine-scale genome-wide signature of Pleistocene glaciation in Thitarodes moths (Lepidoptera: Hepialidae), host of Ophiocordyceps fungus in the Hengduan Mountains. Mol Ecol 2022; 32:2695-2714. [PMID: 35377501 DOI: 10.1111/mec.16457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 02/12/2022] [Accepted: 03/21/2022] [Indexed: 11/28/2022]
Abstract
The Hengduan Mountains region is a biodiversity hotspot known for its topologically complex, deep valleys and high mountains. While landscape and glacial refugia have been evoked to explain patterns of inter-species divergence, the accumulation of intra-species (i.e. population level) genetic divergence across the mountain-valley landscape in this region has received less attention. We used genome-wide restriction site-associated DNA sequencing (RADseq) to reveal signatures of Pleistocene glaciation in populations of Thitarodes shambalaensis (Lepidoptera: Hepialidae), the host moth of parasitic Ophiocordyceps sinensis (Hypocreales: Ophiocordycipitaceae) or "caterpillar fungus" endemic to the glacier of eastern Mt. Gongga. We used moraine history along the glacier valleys to model the distribution and environmental barriers to gene flow across populations of T. shambalaensis. We found that moth populations separated by less than 10 km exhibited valley-based population genetic clustering and isolation-by-distance (IBD), while gene flow among populations was best explained by models using information about their distributions at the local last glacial maximum (LGML , 58 kya), not their contemporary distribution. Maximum likelihood lineage history among populations, and among subpopulations as little as 500 meters apart, recapitulated glaciation history across the landscape. We also found signals of isolated population expansion following the retreat of LGML glaciers. These results reveal the fine-scale, long-term historical influence of landscape and glaciation on the genetic structuring of populations of an endangered and economically important insect species. Similar mechanisms, given enough time and continued isolation, could explain the contribution of glacier refugia to the generation of species diversity among the Hengduan Mountains.
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Affiliation(s)
- Zhengyang Wang
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Naomi E Pierce
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
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Cabrera AA, Schall E, Bérubé M, Anderwald P, Bachmann L, Berrow S, Best PB, Clapham PJ, Cunha H, Dalla Rosa L, Dias C, Findlay K, Haug T, Heide‐Jørgensen MP, Hoelzel A, Kovacs KM, Landry S, Larsen F, Lopes XM, Lydersen C, Mattila DK, Oosting T, Pace RM, Papetti C, Paspati A, Pastene LA, Prieto R, Ramp C, Robbins J, Sears R, Secchi ER, Silva MA, Simon M, Víkingsson G, Wiig Ø, Øien N, Palsbøll PJ. Strong and lasting impacts of past global warming on baleen whales and their prey. GLOBAL CHANGE BIOLOGY 2022; 28:2657-2677. [PMID: 35106859 PMCID: PMC9305191 DOI: 10.1111/gcb.16085] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 05/14/2023]
Abstract
Global warming is affecting the population dynamics and trophic interactions across a wide range of ecosystems and habitats. Translating these real-time effects into their long-term consequences remains a challenge. The rapid and extreme warming period that occurred after the Last Glacial Maximum (LGM) during the Pleistocene-Holocene transition (7-12 thousand years ago) provides an opportunity to gain insights into the long-term responses of natural populations to periods with global warming. The effects of this post-LGM warming period have been assessed in many terrestrial taxa, whereas insights into the impacts of rapid global warming on marine taxa remain limited, especially for megafauna. In order to understand how large-scale climate fluctuations during the post-LGM affected baleen whales and their prey, we conducted an extensive, large-scale analysis of the long-term effects of the post-LGM warming on abundance and inter-ocean connectivity in eight baleen whale and seven prey (fish and invertebrates) species across the Southern and the North Atlantic Ocean; two ocean basins that differ in key oceanographic features. The analysis was based upon 7032 mitochondrial DNA sequences as well as genome-wide DNA sequence variation in 100 individuals. The estimated temporal changes in genetic diversity during the last 30,000 years indicated that most baleen whale populations underwent post-LGM expansions in both ocean basins. The increase in baleen whale abundance during the Holocene was associated with simultaneous changes in their prey and climate. Highly correlated, synchronized and exponential increases in abundance in both baleen whales and their prey in the Southern Ocean were indicative of a dramatic increase in ocean productivity. In contrast, the demographic fluctuations observed in baleen whales and their prey in the North Atlantic Ocean were subtle, varying across taxa and time. Perhaps most important was the observation that the ocean-wide expansions and decreases in abundance that were initiated by the post-LGM global warming, continued for millennia after global temperatures stabilized, reflecting persistent, long-lasting impacts of global warming on marine fauna.
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Affiliation(s)
- Andrea A. Cabrera
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Elena Schall
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Martine Bérubé
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- Center for Coastal StudiesProvincetownMassachusettsUSA
| | - Pia Anderwald
- Swiss National ParkChastè Planta‐WildenbergZernezSwitzerland
| | | | - Simon Berrow
- Marine and Freshwater Research CentreGalway‐Mayo Institute of TechnologyGalwayIreland
- Irish Whale and Dolphin GroupMerchants QuayKilrushCounty ClareIreland
| | - Peter B. Best
- Department of Zoology and EntomologyMammal Research InstituteUniversity of PretoriaHatfieldSouth Africa
| | | | - Haydée A. Cunha
- Aquatic Mammals and Bioindicators Laboratory (MAQUA)Faculty of OceanographyState University of Rio de Janeiro ‐ UERJMaracanãRio de JaneiroBrazil
- Genetics Department of the Biology InstituteState University of Rio de Janeiro ‐ UERJMaracanãRio de JaneiroBrazil
| | - Luciano Dalla Rosa
- Laboratory of Ecology and Conservation of Marine MegafaunaInstitute of OceanographyFederal University of Rio Grande‐FURGRio GrandeRio Grande do SulBrazil
| | - Carolina Dias
- Aquatic Mammals and Bioindicators Laboratory (MAQUA)Faculty of OceanographyState University of Rio de Janeiro ‐ UERJMaracanãRio de JaneiroBrazil
| | - Kenneth P. Findlay
- Department of Zoology and EntomologyMammal Research InstituteUniversity of PretoriaHatfieldSouth Africa
- Department Conservation and Marine SciencesCentre for Sustainable Oceans EconomyCape Peninsula University of TechnologyCape TownSouth Africa
| | - Tore Haug
- Research Group Marine MammalsInstitute of Marine ResearchTromsøNorway
| | | | | | | | - Scott Landry
- Center for Coastal StudiesProvincetownMassachusettsUSA
| | - Finn Larsen
- Section for Ecosystem based Marine ManagementNational Institute of Aquatic ResourcesTechnical University of DenmarkKongens LyngbyDenmark
| | - Xênia M. Lopes
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | | | | | - Tom Oosting
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Richard M. Pace
- Northeast Fisheries Science CenterNational Marine Fisheries ServiceWoods HoleMassachusettsUSA
| | | | - Angeliki Paspati
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- Hellenic Agricultural Organisation‐“DIMITRA”HerakleionCreteGreece
| | | | - Rui Prieto
- Institute of Marine Sciences – Okeanos & Institute of Marine Research ‐ IMARUniversity of the AzoresHortaPortugal
| | - Christian Ramp
- Sea Mammal Research UnitScottish Oceans InstituteUniversity of St. AndrewsScotlandUK
- Mingan Island Cetacean StudySaint LambertQuébecCanada
| | - Jooke Robbins
- Center for Coastal StudiesProvincetownMassachusettsUSA
| | - Richard Sears
- Greenland Climate Research CentreGreenland Institute of Natural ResourcesNuukGreenland
| | - Eduardo R. Secchi
- Laboratory of Ecology and Conservation of Marine MegafaunaInstitute of OceanographyFederal University of Rio Grande‐FURGRio GrandeRio Grande do SulBrazil
| | - Mónica A. Silva
- Institute of Marine Sciences – Okeanos & Institute of Marine Research ‐ IMARUniversity of the AzoresHortaPortugal
| | - Malene Simon
- Greenland Climate Research CentreGreenland Institute of Natural ResourcesNuukGreenland
| | | | - Øystein Wiig
- Natural History MuseumUniversity of OsloOsloNorway
| | - Nils Øien
- Marine Mammal DivisionInstitute of Marine ResearchBergenNorway
| | - Per J. Palsbøll
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- Center for Coastal StudiesProvincetownMassachusettsUSA
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Late Pleistocene pottery production and exchange: Provenance studies of hunter-gatherer wares from southern Kyushu, Japan by neutron activation analysis. PLoS One 2022; 17:e0265329. [PMID: 35294491 PMCID: PMC8926207 DOI: 10.1371/journal.pone.0265329] [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: 11/05/2021] [Accepted: 02/28/2022] [Indexed: 11/19/2022] Open
Abstract
Late Pleistocene hunter-gatherers in East Asia adopted pottery, yet the ability to reconstruct circulation, mobility, and exchange has been hampered, in part, due to problematic regional geochronology. The driving forces behind pottery adoption is unclear. The purpose of this study is to test our results of the first systematic petrographic pottery sourcing from the pre-Younger Dryas by utilizing neutron activation analysis. We examine samples from the Sankauyama I site on Tanegashima Island, southern Japan, dating to the Incipient Jomon, ca. 14,000/13,500–12,800 cal BP, with a well-defined geochronology. Our NAA results corroborate with the petrographic study suggesting that pottery was mainly produced in-situ, but some vessels were transported long distances from another island. Changing from high mobility, sedentary Incipient Jomon foragers made pottery, occasionally investing in long-distance ceramic vessel transportation and exchange likely involving ocean crossing. This may be associated with a risk-buffering strategy in the context of rising sea levels and isolation of Tanegashima.
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Morris CE, Ramirez N, Berge O, Lacroix C, Monteil C, Chandeysson C, Guilbaud C, Blischke A, Sigurbjörnsdóttir MA, Vilhelmsson OÞ. Pseudomonas syringae on Plants in Iceland Has Likely Evolved for Several Million Years Outside the Reach of Processes That Mix This Bacterial Complex across Earth’s Temperate Zones. Pathogens 2022; 11:pathogens11030357. [PMID: 35335680 PMCID: PMC8951587 DOI: 10.3390/pathogens11030357] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 12/04/2022] Open
Abstract
Here we report, for the first time, the occurrence of the bacteria from the species complex Pseudomonas syringae in Iceland. We isolated this bacterium from 35 of the 38 samples of angiosperms, moss, ferns and leaf litter collected across the island from five habitat categories (boreal heath, forest, subalpine and glacial scrub, grazed pasture, lava field). The culturable populations of P. syringae on these plants varied in size across 6 orders of magnitude, were as dense as 107 cfu g−1 and were composed of strains in phylogroups 1, 2, 4, 6, 7, 10 and 13. P. syringae densities were significantly greatest on monocots compared to those on dicots and mosses and were about two orders of magnitude greater in grazed pastures compared to all other habitats. The phylogenetic diversity of 609 strains of P. syringae from Iceland was compared to that of 933 reference strains of P. syringae from crops and environmental reservoirs collected from 27 other countries based on a 343 bp sequence of the citrate synthase (cts) housekeeping gene. Whereas there were examples of identical cts sequences across multiple countries and continents among the reference strains indicating mixing among these countries and continents, the Icelandic strains grouped into monophyletic lineages that were unique compared to all of the reference strains. Based on estimates of the time of divergence of the Icelandic genetic lineages of P. syringae, the geological, botanical and land use history of Iceland, and atmospheric circulation patterns, we propose scenarios whereby it would be feasible for P. syringae to have evolved outside the reach of processes that tend to mix this bacterial complex across the planet elsewhere.
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Affiliation(s)
- Cindy E. Morris
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
- Correspondence:
| | - Natalia Ramirez
- Faculty of Natural Resource Sciences, University of Akureyri, 600 Akureyri, Iceland; (N.R.); (M.A.S.); (O.Þ.V.)
| | - Odile Berge
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
| | - Christelle Lacroix
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
| | - Cécile Monteil
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
| | - Charlotte Chandeysson
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
| | - Caroline Guilbaud
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
| | - Anett Blischke
- ÍSOR, Iceland GeoSurvey, Rangárvöllum við Hlíðarfjallsveg, 600 Akureyri, Iceland;
| | | | - Oddur Þ. Vilhelmsson
- Faculty of Natural Resource Sciences, University of Akureyri, 600 Akureyri, Iceland; (N.R.); (M.A.S.); (O.Þ.V.)
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Palaeo-Shoreline Configuration of the Adventure Plateau (Sicilian Channel) at the Last Glacial Maximum. GEOSCIENCES 2022. [DOI: 10.3390/geosciences12030125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Adventure Plateau, located in the NW sector of the Sicilian Channel, experienced several episodes of exposure/erosion and subsequent drowning, with the most recent occurring after the Last Glacial Maximum (LGM). Unlike other parts of the Sicilian Channel, the Adventure Plateau is relatively tectonically stable and is therefore best suitable for reconstructing its coastal configuration before the post-LGM marine transgression. Here, we use high-resolution seismic data to identify and map the palaeo-coastline at the LGM on the basis of the internal architecture of the prograding wedges (i.e., the location of the subaqueous clinoform rollover point) and the erosional markers such as the subaerial unconformities and the wave ravinement surfaces. These data, which show an extreme variability in the palaeo-morphology of the coastal margins of the Adventure Plateau, have been complemented with vintage seismic profiles in order to entirely cover its perimeter. The mapped LGM coastline has then been compared to predictions from glacial isostatic adjustment (GIA) modeling, which considers the horizontal migration of the shorelines in response to sea level rise and to Earth’s rotational and deformational effects associated with deglaciation. The two shorelines (i.e., the coastline derived from the marine data interpretation and the one derived from the GIA model) are in good agreement at 21 kyears BP, although some discrepancies occur in the southern part of the plateau, where the seabed slope is extremely gentle, which makes the clinoform rollover points and the buried erosional unconformities difficult to detect. After 20 kyears BP, an acceleration in the rate of the sea level rise occurred. The results of this study indicate the importance of comparing experimental data with model predictions in order to refine and calibrate boundary parameters and to gain a better picture of the evolution of sea level rise over various time scales.
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136
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Balmori-de la Puente A, Ventura J, Miñarro M, Somoano A, Hey J, Castresana J. Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola. Sci Rep 2022; 12:4065. [PMID: 35260719 PMCID: PMC8904462 DOI: 10.1038/s41598-022-07877-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/21/2022] [Indexed: 01/18/2023] Open
Abstract
Molecular dating methods of population splits are crucial in evolutionary biology, but they present important difficulties due to the complexity of the genealogical relationships of genes and past migrations between populations. Using the double digest restriction-site associated DNA (ddRAD) technique and an isolation-with-migration (IM) model, we studied the evolutionary history of water vole populations of the genus Arvicola, a group of complex evolution with fossorial and semi-aquatic ecotypes. To do this, we first estimated mutation rates of ddRAD loci using a phylogenetic approach. An IM model was then used to estimate split times and other relevant demographic parameters. A set of 300 ddRAD loci that included 85 calibrated loci resulted in good mixing and model convergence. The results showed that the two populations of A. scherman present in the Iberian Peninsula split 34 thousand years ago, during the last glaciation. In addition, the much greater divergence from its sister species, A. amphibius, may help to clarify the controversial taxonomy of the genus. We conclude that this approach, based on ddRAD data and an IM model, is highly useful for analyzing the origin of populations and species.
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Affiliation(s)
- Alfonso Balmori-de la Puente
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003, Barcelona, Spain
| | - Jacint Ventura
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain.,Àrea de Recerca en Petits Mamífers, Granollers Museum of Natural Sciences, Palaudàries, 102, 08402, Granollers, Barcelona, Spain
| | - Marcos Miñarro
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Ctra AS-267, PK 19, 33300, Villaviciosa, Asturias, Spain
| | - Aitor Somoano
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Ctra AS-267, PK 19, 33300, Villaviciosa, Asturias, Spain
| | - Jody Hey
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003, Barcelona, Spain.
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137
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Rosetti N, Krohling D, Remis MI. Evolutionary history and colonization patterns of the wing dimorphic grasshopper Dichroplus vittatus in two Argentinean biomes. Sci Rep 2022; 12:2920. [PMID: 35190570 PMCID: PMC8861051 DOI: 10.1038/s41598-022-05162-6] [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: 07/30/2021] [Accepted: 12/30/2021] [Indexed: 12/03/2022] Open
Abstract
Quaternary climate oscillations and modification of the environment by humans have played an important role in shaping species distribution and genetic structure of modern species. Here, population genetic parameters were inferred from the analysis of 168 individuals belonging to 11 populations of the South American grasshopper, Dichroplus vittatus, distributed in two Argentinean Biomes (Grassland and Savanna), by sequencing a 543 bp of the mitochondrial COI gene. Overall, we detected considerable haplotype diversity and low nucleotide diversity. AMOVA analyses showed a significant degree of differentiation among Biomes and between populations. Two major mitochondrial lineages can be distinguished. The haplogroup containing the most common haplotype split 17,000 years BP while the haplogroup including the second most common haplotype has a divergence date of about 11,700 years. Approximate Bayesian Computation (ABC) analyses showed that the palaeodemographic scenario that best fitted our data is consistent with a hypothesis of divergence from an ancestral population and subsequent admixture with Grassland-Savanna (South–North) direction. Our results suggest that populations located in both Biomes would derive from a single ancestral population that colonized the region after the Last Glacial Maximum and Grassland would have a more ancestral origin than Savanna. Further, our results emphasize the importance of human-mediated dispersal in the reconfiguration of genetic diversity of species with potential pest capacity.
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138
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Yang F, Cai L, Dao Z, Sun W. Genomic Data Reveals Population Genetic and Demographic History of Magnolia fistulosa (Magnoliaceae), a Plant Species With Extremely Small Populations in Yunnan Province, China. FRONTIERS IN PLANT SCIENCE 2022; 13:811312. [PMID: 35251084 PMCID: PMC8892343 DOI: 10.3389/fpls.2022.811312] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/13/2022] [Indexed: 05/11/2023]
Abstract
Elucidating the genetic background of threatened species is fundamental to their management and conservation, and investigating the demographic history of these species is helpful in the determination of the threats facing them. The woody species of the genus Magnolia (Magnoliaceae) have high economic, scientific and ecological values. Although nearly half of all Magnolia species have been evaluated as threatened, to date there has been no population genetic study employing Next Generation Sequencing (NGS) technology in this genus. In the present study, we investigate the conservation genomics of Magnolia fistulosa, a threatened species endemic to the limestone area along the Sino-Vietnamese border, using a double digest restriction-site-associated DNA-sequencing (ddRAD-seq) approach. To increase the reliability of our statistical inferences, we employed two approaches, Stacks and ipyrad, for SNP calling. A total of 15,272 and 18,960, respectively, putatively neutral SNPs were generated by Stacks and ipyrad. Relatively high genetic diversity and large population divergence were detected in M. fistulosa. Although higher absolute values were calculated using the ipyrad data set, the two data sets showed the same trends in genetic diversity (π, H e), population differentiation (F ST) and inbreeding coefficients (F IS). A change in the effective population size of M. fistulosa within the last 1 Ma was detected, including a population decline about 0.5-0.8 Ma ago, a bottleneck event about 0.2-0.3 Ma ago, population fluctuations during the last glacial stage, and the recovery of effective population size after the last glacial maximum. Our findings not only lay the foundation for the future conservation of this species, but also provide new insights into the evolutionary history of the genus Magnolia in southeastern Yunnan, China.
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Affiliation(s)
- Fengmao Yang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Lei Cai
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhiling Dao
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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139
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Population genomic signatures of the oriental fruit moth related to the Pleistocene climates. Commun Biol 2022; 5:142. [PMID: 35177826 PMCID: PMC8854661 DOI: 10.1038/s42003-022-03097-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/31/2022] [Indexed: 12/31/2022] Open
Abstract
The Quaternary climatic oscillations are expected to have had strong impacts on the evolution of species. Although legacies of the Quaternary climates on population processes have been widely identified in diverse groups of species, adaptive genetic changes shaped during the Quaternary have been harder to decipher. Here, we assembled a chromosome-level genome of the oriental fruit moth and compared genomic variation among refugial and colonized populations of this species that diverged in the Pleistocene. High genomic diversity was maintained in refugial populations. Demographic analysis showed that the effective population size of refugial populations declined during the penultimate glacial maximum (PGM) but remained stable during the last glacial maximum (LGM), indicating a strong impact of the PGM rather than the LGM on this pest species. Genome scans identified one chromosomal inversion and a mutation of the circadian gene Clk on the neo-Z chromosome potentially related to the endemicity of a refugial population. In the colonized populations, genes in pathways of energy metabolism and wing development showed signatures of selection. These different genomic signatures of refugial and colonized populations point to multiple impacts of Quaternary climates on adaptation in an extant species. The oriental fruit moth is a pest species native to East Asia with refugial and colonized populations throughout the region. Here, a chromosome-level assembly for the species is reported and used to identify genomic signatures related to Quaternary climate change.
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140
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Walkup DK, Lawing AM, Hibbitts TJ, Ryberg WA. Biogeographic consequences of shifting climate for the western massasauga (
Sistrurus tergeminus
). Ecol Evol 2022; 12:e8599. [PMID: 35169456 PMCID: PMC8831096 DOI: 10.1002/ece3.8599] [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: 11/30/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 11/20/2022] Open
Abstract
The western massasauga (Sistrurus tergeminus) is a small pit viper with an extensive geographic range, yet observations of this species are relatively rare. They persist in patchy and isolated populations, threatened by habitat destruction and fragmentation, mortality from vehicle collisions, and deliberate extermination. Changing climates may pose an additional stressor on the survival of isolated populations. Here, we evaluate historic, modern, and future geographic projections of suitable climate for S. tergeminus to outline shifts in their potential geographic distribution and inform current and future management. We used maximum entropy modeling to build multiple models of the potential geographic distribution of S. tergeminus. We evaluated the influence of five key decisions made during the modeling process on the resulting geographic projections of the potential distribution, allowing us to identify areas of model robustness and uncertainty. We evaluated models with the area under the receiver operating curve and true skill statistic. We retained 16 models to project both in the past and future multiple general circulation models. At the last glacial maximum, the potential geographic distribution associated with S. tergeminus occurrences had a stronghold in the southern part of its current range and extended further south into Mexico, but by the mid‐Holocene, its modeled potential distribution was similar to its present‐day potential distribution. Under future model projections, the potential distribution of S. tergeminus moves north, with the strongest northward trends predicted under a climate scenario increase of 8.5 W/m2. Some southern populations of S. tergeminus have likely already been extirpated and will continue to be threatened by shifting availability of suitable climate, as they are already under threat from desertification of grasslands. Land use and habitat loss at the northern edge of the species range are likely to make it challenging for this species to track suitable climates northward over time.
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Affiliation(s)
| | - Anna Michelle Lawing
- Department of Ecology and Conservation Biology Texas A&M University College Station Texas USA
| | - Toby J. Hibbitts
- Texas A&M Natural Resources Institute College Station Texas USA
- Biodiversity Research and Teaching Collection Department of Ecology and Conservation Biology Texas A&M University College Station Texas USA
| | - Wade A. Ryberg
- Texas A&M Natural Resources Institute College Station Texas USA
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141
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Koot E, Arnst E, Taane M, Goldsmith K, Thrimawithana A, Reihana K, González-Martínez SC, Goldsmith V, Houliston G, Chagné D. Genome-wide patterns of genetic diversity, population structure and demographic history in mānuka (Leptospermum scoparium) growing on indigenous Māori land. HORTICULTURE RESEARCH 2022; 9:uhab012. [PMID: 35039864 PMCID: PMC8771449 DOI: 10.1093/hr/uhab012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/09/2021] [Accepted: 09/02/2021] [Indexed: 06/14/2023]
Abstract
Leptospermum scoparium J. R. Forst et G. Forst, known as mānuka by Māori, the indigenous people of Aotearoa (New Zealand), is a culturally and economically significant shrub species, native to New Zealand and Australia. Chemical, morphological and phylogenetic studies have indicated geographical variation of mānuka across its range in New Zealand, and genetic differentiation between New Zealand and Australia. We used pooled whole genome re-sequencing of 76 L. scoparium and outgroup populations from New Zealand and Australia to compile a dataset totalling ~2.5 million SNPs. We explored the genetic structure and relatedness of L. scoparium across New Zealand, and between populations in New Zealand and Australia, as well as the complex demographic history of this species. Our population genomic investigation suggests there are five geographically distinct mānuka gene pools within New Zealand, with evidence of gene flow occurring between these pools. Demographic modelling suggests three of these gene pools have undergone expansion events, whilst the evolutionary histories of the remaining two have been subjected to contractions. Furthermore, mānuka populations in New Zealand are genetically distinct from populations in Australia, with coalescent modelling suggesting these two clades diverged ~9-12 million years ago. We discuss the evolutionary history of this species and the benefits of using pool-seq for such studies. Our research will support the management and conservation of mānuka by landowners, particularly Māori, and the development of a provenance story for the branding of mānuka based products.
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Affiliation(s)
- Emily Koot
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Batchelar Rd, Palmerston North 4410, New Zealand
| | - Elise Arnst
- Manaaki Whenua Landcare Research, 54 Gerald St, Lincoln 7608, New Zealand
| | - Melissa Taane
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Batchelar Rd, Palmerston North 4410, New Zealand
| | | | | | - Kiri Reihana
- Manaaki Whenua Landcare Research, 54 Gerald St, Lincoln 7608, New Zealand
| | | | | | - Gary Houliston
- Manaaki Whenua Landcare Research, 54 Gerald St, Lincoln 7608, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Batchelar Rd, Palmerston North 4410, New Zealand
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142
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Golikova E, Korsun S, Voltski I, Varfolomeeva M, Granovitch A. High-Arctic intertidal foraminifera, 78°N Spitsbergen. Polar Biol 2022. [DOI: 10.1007/s00300-021-02967-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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143
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Chen YJ, Zhu L, Wu QN, Hu CC, Qu YF, Ji X. Geological and climatic influences on population differentiation of the Phrynocephalus vlangalii species complex (Sauria: Agamidae) in the northern Qinghai-Tibet Plateau. Mol Phylogenet Evol 2022; 169:107394. [PMID: 35045310 DOI: 10.1016/j.ympev.2022.107394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/06/2021] [Accepted: 12/25/2021] [Indexed: 11/26/2022]
Abstract
Extremely heterogeneous topography and complex paleoclimate history of the Qinghai-Tibet Plateau (QTP) have a key role in promoting genetic divergence and lineage/species formation. Here, we sequenced one nuclear and three mitochondrial markers of 532 individuals from the entire range of the Phrynocephalus vlangalii species complex including two species, P. putjatai and P. vlangalii, endemic to the northern QTP. We integrated multilocus phylogeny, demographic analysis and geographic barrier detection to evaluate the population structure and dynamics. We found a new mitochondrial clade (PV-I) in the Gonghe County population of P. vlangalii, partial mitochondrial DNA replacement within P. vlangalii and complete mitochondrial DNA replacement between P. putjatai and P. vlangalii. Neutrality test, mismatch distribution analysis and Extended Bayesian Skyline Plot (EBSP) analysis all supported a significant expansion of the Qaidam Basin population of P. vlangalii (PV-II-2) from 0.091 to 0.026 Ma after Penultimate Glaciation. The uplift of the Arjin and Anyemanqen Mountains during the Kunhuang Movement (∼1.2 Ma) split populations of P. vlangalii in Akesai, Qaidam Basin and source of the Yellow River. The uplift of the Elashan Mountains during the second phase of the Qingzang Movement (∼2.5 Ma) contributed to the divergence of the Gonghe County population of P. vlangalii from other conspecific populations. The third phase of the Qingzang Movement (∼1.7 Ma) contributed to the divergence of the Xinghai population of P. vlangalii from P. putjatai and to the divergence of the northern populations of P. putjatai from the southern conspecific populations. Our data support the idea that the geological and climatic changes following the orogeny of the QTP may have promoted population differentiation and shaped the current population patterns of the P. vlangalii species complex in the northeastern QTP.
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Affiliation(s)
- Yi-Jing Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Lin Zhu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Qian-Nian Wu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Chao-Chao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China.
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, China; College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, Zhejiang, China.
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144
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Murchie TJ, Karpinski E, Eaton K, Duggan AT, Baleka S, Zazula G, MacPhee RDE, Froese D, Poinar HN. Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments. Curr Biol 2022; 32:851-860.e7. [PMID: 35016010 DOI: 10.1016/j.cub.2021.12.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/20/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022]
Abstract
Traditionally, paleontologists have relied on the morphological features of bones and teeth to reconstruct the evolutionary relationships of extinct animals.1 In recent decades, the analysis of ancient DNA recovered from macrofossils has provided a powerful means to evaluate these hypotheses and develop novel phylogenetic models.2 Although a great deal of life history data can be extracted from bones, their scarcity and associated biases limit their information potential. The paleontological record of Beringia3-the unglaciated areas and former land bridge between northeast Eurasia and northwest North America-is relatively robust thanks to its perennially frozen ground favoring fossil preservation.4,5 However, even here, the macrofossil record is significantly lacking in small-bodied fauna (e.g., rodents and birds), whereas questions related to migration and extirpation, even among well-studied taxa, remain crudely resolved. The growing sophistication of ancient environmental DNA (eDNA) methods have allowed for the identification of species within terrestrial/aquatic ecosystems,6-12 in paleodietary reconstructions,13-19 and facilitated genomic reconstructions from cave contexts.8,20-22 Murchie et al.6,23 used a capture enrichment approach to sequence a diverse range of faunal and floral DNA from permafrost silts deposited during the Pleistocene-Holocene transition.24 Here, we expand on their work with the mitogenomic assembly and phylogenetic placement of Equus caballus (caballine horse), Bison priscus (steppe bison), Mammuthus primigenius (woolly mammoth), and Lagopus lagopus (willow ptarmigan) eDNA from multiple permafrost cores spanning the last 30,000 years. We identify a diverse metagenomic spectra of Pleistocene fauna and identify the eDNA co-occurrence of distinct Eurasian and American mitogenomic lineages.
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Affiliation(s)
- Tyler J Murchie
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada.
| | - Emil Karpinski
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Katherine Eaton
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Ana T Duggan
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Sina Baleka
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Grant Zazula
- Yukon Government, Palaeontology Program, Department of Tourism and Culture, Box 2703, Whitehorse, YT Y1A 2C6, Canada; Collections and Research, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, ON K1P 6P4, Canada
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USA
| | - Duane Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB T6G 2E3, Canada.
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; CIFAR, Humans and the Microbiome Program, MaRS Centre, West Tower, 661 University Avenue, Suite 505, Toronto, ON M5G 1M1, Canada.
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145
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Liang YY, Shi Y, Yuan S, Zhou BF, Chen XY, An QQ, Ingvarsson PK, Plomion C, Wang B. Linked selection shapes the landscape of genomic variation in three oak species. THE NEW PHYTOLOGIST 2022; 233:555-568. [PMID: 34637540 DOI: 10.1111/nph.17793] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Natural selection shapes genome-wide patterns of diversity within species and divergence between species. However, quantifying the efficacy of selection and elucidating the relative importance of different types of selection in shaping genomic variation remain challenging. We sequenced whole genomes of 101 individuals of three closely related oak species to track the divergence history, and to dissect the impacts of selective sweeps and background selection on patterns of genomic variation. We estimated that the three species diverged around the late Neogene and experienced a bottleneck during the Pleistocene. We detected genomic regions with elevated relative differentiation ('FST -islands'). Population genetic inferences from the site frequency spectrum and ancestral recombination graph indicated that FST -islands were formed by selective sweeps. We also found extensive positive selection; the fixation of adaptive mutations and reduction neutral diversity around substitutions generated a signature of selective sweeps. Prevalent negative selection and background selection have reduced genetic diversity in both genic and intergenic regions, and contributed substantially to the baseline variation in genetic diversity. Our results demonstrate the importance of linked selection in shaping genomic variation, and illustrate how the extent and strength of different selection models vary across the genome.
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Affiliation(s)
- Yi-Ye Liang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Shuai Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Biao-Feng Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xue-Yan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Qing-Qing An
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | | | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
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146
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Honka J, Baini S, Searle JB, Kvist L, Aspi J. Genetic assessment reveals inbreeding, possible hybridization, and low levels of genetic structure in a declining goose population. Ecol Evol 2022; 12:e8547. [PMID: 35127046 PMCID: PMC8796947 DOI: 10.1002/ece3.8547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022] Open
Abstract
The population numbers of taiga bean goose (Anser fabalis fabalis) have halved during recent decades. Since this subspecies is hunted throughout most of its range, the decline is of management concern. Knowledge of the genetic population structure and diversity is important for guiding management and conservation efforts. Genetically unique subpopulations might be hunted to extinction if not managed separately, and any inbreeding depression or lack of genetic diversity may affect the ability to adapt to changing environments and increase extinction risk. We used microsatellite and mitochondrial DNA markers to study the genetic population structure and diversity among taiga bean geese breeding within the Central flyway management unit using non-invasively collected feathers. We found some genetic structuring with the maternally inherited mitochondrial DNA between four geographic regions (ɸ ST = 0.11-0.20) but none with the nuclear microsatellite markers (all pairwise F ST-values = 0.002-0.005). These results could be explained by female natal philopatry and male-biased dispersal, which completely homogenizes the nuclear genome. Therefore, the population could be managed as a single unit. Genetic diversity was still at a moderate level (average H E = 0.69) and there were no signs of past population size reductions, although significantly positive inbreeding coefficients in all sampling sites (F IS = 0.05-0.10) and high relatedness values (r = 0.60-0.86) between some individuals could indicate inbreeding. In addition, there was evidence of either incomplete lineage sorting or introgression from the pink-footed goose (Anser brachyrhynchus). The current population is not under threat by genetic impoverishment but monitoring in the future is desirable.
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Affiliation(s)
- Johanna Honka
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Serena Baini
- Department of BiologyUniversity of Rome “Tor Vergata”RomeItaly
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew YorkUSA
| | - Laura Kvist
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Jouni Aspi
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
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147
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The impact of prehistoric human dispersals on the presence of tobacco-related oral cancer in Northeast India. Gene 2021; 813:146098. [PMID: 34952175 DOI: 10.1016/j.gene.2021.146098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/20/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Northeast (NE) India is a subject of debate for predicting its involvement in prehistoric anatomically modern human (AMH) dispersal. The unique lifestyle and genetic characteristics of native ethnic groups in this region are believed to be responsible for their susceptibility to tobacco-related oral cancer (TrOC). The present study assessed mitochondrial macro-haplogroup (mHG) diversity and TrOC susceptibility autosomal loci to evaluate the impact of prehistoric AMH dispersal on the present day's high TrOC prevalence in major NE Indian ethnics. METHODS We considered 175 unrelated individuals from 35 ethnic groups and previously published 374 sequences for sequencing-based assessment of mtDNA-based marker by subsequent analyses like haplogroup diversity, phylogenetic, genetic structure by AMOVA, and MDS, descriptive statistics of demographic parameters, and migration analysis. Besides, we selected prolonged tobacco-chewing 124 case-control individuals from similar ethnic backgrounds for genotyping 115 autosomal loci in Sequenom iPLEX MassARRAY™ platform and mined 1000genome data (n = 398) for consequent global admixture and ancestry-specific allele frequencies-based analyses. RESULTS Our mtDNA-based findings suggested that NE populations were distinct from other Indian populations, owing to the first wave of migration from ancient southern China (∼54kya) and two successive spatial expansion events at ∼45kya and ∼43kya. Consequently, it probably acted as another source for prehistoric AMH dispersal in N/NE Asia. Besides, the second wave of back-migration from SE Asia (∼40kya) probably replaced the mitochondrial footprints of survivors from the first migrants and introduced the TrOC susceptibility traits in this region. Afterward, the autosomal marker-based observations on the transition of the disease-associated admixture component 'K6' from SE Asia reconfirmed these results. Moreover, we also observed that the mitochondrial mHG 'R' is significantly associated with the risk of TrOC (OR > 9.5) in NE India. Furthermore, the possible onset of the phenotypic expression of those traits was predicted at ∼4kya, thus, contributing to present-day's TrOC prevalence. CONCLUSIONS This study reflects its uniqueness by revealing an updated AMH dispersal route for the peopling in and out of NE India, which probably introduced the disease-causing traits in the ancestral NE Indian population. Those traits were then imprinted in their genome to get transferred through their respective generations, forming the present-day's TrOC-prevalent NE Indian population.
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148
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Integrative geochronology calibrates the Middle and Late Stone Ages of Ethiopia's Afar Rift. Proc Natl Acad Sci U S A 2021; 118:2116329118. [PMID: 34873047 PMCID: PMC8685921 DOI: 10.1073/pnas.2116329118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 01/19/2023] Open
Abstract
Understanding the evolution, dispersals, behaviors, and ecologies of early African Homo sapiens requires accurate geochronological placement of fossils and artifacts. We introduce open-air occurrences of such remains in sediments of the Middle Awash study area in Ethiopia. We describe the stratigraphic and depositional contexts of our discoveries and demonstrate the effectiveness of recently developed uranium-series dating of ostrich eggshell at validating and bridging across more traditional radioisotopic methods (14C and 40Ar/39Ar). Homo sapiens fossils and associated Middle Stone Age artifacts are placed at >158 and ∼96 ka. Later Stone Age occurrences are dated to ∼21 to 24 ka and ∼31 to 32 ka, firmly dating the upper portion of one of the longest records of human evolution. The Halibee member of the Upper Dawaitoli Formation of Ethiopia’s Middle Awash study area features a wealth of Middle and Later Stone Age (MSA and LSA) paleoanthropological resources in a succession of Pleistocene sediments. We introduce these artifacts and fossils, and determine their chronostratigraphic placement via a combination of established radioisotopic methods and a recently developed dating method applied to ostrich eggshell (OES). We apply the recently developed 230Th/U burial dating of OES to bridge the temporal gap between radiocarbon (14C) and 40Ar/39Ar ages for the MSA and provide 14C ages to constrain the younger LSA archaeology and fauna to ∼24 to 21.4 ka. Paired 14C and 230Th/U burial ages of OES agree at ∼31 ka for an older LSA locality, validating the newer method, and in turn supporting its application to stratigraphically underlying MSA occurrences previously constrained only by a maximum 40Ar/39Ar age. Associated fauna, flora, and Homo sapiens fossils are thereby now fixed between 106 ± 20 ka and 96.4 ± 1.6 ka (all errors 2σ). Additional 40Ar/39 results on an underlying tuff refine its age to 158.1 ± 11.0 ka, providing a more precise minimum age for MSA lithic artifacts, fauna, and H. sapiens fossils recovered ∼9 m below it. These results demonstrate how chronological control can be obtained in tectonically active and stratigraphically complex settings to precisely calibrate crucial evidence of technological, environmental, and evolutionary changes during the African Middle and Late Pleistocene.
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149
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Murchie TJ, Monteath AJ, Mahony ME, Long GS, Cocker S, Sadoway T, Karpinski E, Zazula G, MacPhee RDE, Froese D, Poinar HN. Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA. Nat Commun 2021; 12:7120. [PMID: 34880234 PMCID: PMC8654998 DOI: 10.1038/s41467-021-27439-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 11/22/2021] [Indexed: 12/30/2022] Open
Abstract
The temporal and spatial coarseness of megafaunal fossil records complicates attempts to to disentangle the relative impacts of climate change, ecosystem restructuring, and human activities associated with the Late Quaternary extinctions. Advances in the extraction and identification of ancient DNA that was shed into the environment and preserved for millennia in sediment now provides a way to augment discontinuous palaeontological assemblages. Here, we present a 30,000-year sedimentary ancient DNA (sedaDNA) record derived from loessal permafrost silts in the Klondike region of Yukon, Canada. We observe a substantial turnover in ecosystem composition between 13,500 and 10,000 calendar years ago with the rise of woody shrubs and the disappearance of the mammoth-steppe (steppe-tundra) ecosystem. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) at multiple sites persisting thousands of years after their supposed extinction from the fossil record.
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Affiliation(s)
- Tyler J Murchie
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada. .,Department of Anthropology, McMaster University, Hamilton, Canada.
| | - Alistair J Monteath
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada.,School of Geography and Environmental Science, University of Southampton, Southampton, United Kingdom
| | - Matthew E Mahony
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - George S Long
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada
| | - Scott Cocker
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - Tara Sadoway
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,The Hospital for Sick Children, Toronto, Canada
| | - Emil Karpinski
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada
| | - Grant Zazula
- Yukon Government, Palaeontology Program, Department of Tourism and Culture, Whitehorse, Canada.,Collections and Research, Canadian Museum of Nature, Ottawa, Canada
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, New York, United States
| | - Duane Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada.
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, Hamilton, Canada. .,Department of Anthropology, McMaster University, Hamilton, Canada. .,Department of Biochemistry, McMaster University, Hamilton, Canada. .,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada. .,CIFAR Humans and the Microbiome Program, Toronto, Canada.
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150
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Cumer T, Machado AP, Dumont G, Bontzorlos V, Ceccherelli R, Charter M, Dichmann K, Kassinis N, Lourenço R, Manzia F, Martens HD, Prévost L, Rakovic M, Roque I, Siverio F, Roulin A, Goudet J. Landscape and climatic variations shaped secondary contacts amid barn owls of the Western Palearctic. Mol Biol Evol 2021; 39:6454100. [PMID: 34893883 PMCID: PMC8789042 DOI: 10.1093/molbev/msab343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The combined actions of climatic variations and landscape barriers shape the history of natural populations. When organisms follow their shifting niches, obstacles in the landscape can lead to the splitting of populations, on which evolution will then act independently. When two such populations are reunited, secondary contact occurs in a broad range of admixture patterns, from narrow hybrid zones to the complete dissolution of lineages. A previous study suggested that barn owls colonized the Western Palearctic after the last glaciation in a ring-like fashion around the Mediterranean Sea, and conjectured an admixture zone in the Balkans. Here, we take advantage of whole-genome sequences of 94 individuals across the Western Palearctic to reveal the complex history of the species in the region using observational and modeling approaches. Even though our results confirm that two distinct lineages colonized the region, one in Europe and one in the Levant, they suggest that it predates the last glaciation and identify a secondary contact zone between the two in Anatolia. We also show that barn owls recolonized Europe after the glaciation from two distinct glacial refugia: a previously identified western one in Iberia and a new eastern one in Italy. Both glacial lineages now communicate via eastern Europe, in a wide and permeable contact zone. This complex history of populations enlightens the taxonomy of Tyto alba in the region, highlights the key role played by mountain ranges and large water bodies as barriers and illustrates the power of population genomics in uncovering intricate demographic patterns.
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Affiliation(s)
- Tristan Cumer
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ana Paula Machado
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Guillaume Dumont
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Vasileios Bontzorlos
- Green Fund, Kifisia, Athens, Greece.,"TYTO" - Organization for the Management and Conservation of Biodiversity in Agricultural Ecosystems, Larisa, Greece
| | | | - Motti Charter
- Shamir Research Institute, University of Haifa, Katzrin, Israel.,Department of Geography and Environmental Sciences, University of Haifa, Haifa, Israel
| | | | | | - Rui Lourenço
- MED Mediterranean Institute for Agriculture, Environment and Development, Laboratory of Ornithology, IIFA, University of Évora, Évora, Portugal
| | | | | | - Laure Prévost
- Association C.H.E.N.E, Centre d'Hébergement et d'Etude sur la Nature et l'Environnement, Allouville-Bellefosse, 76190, France
| | - Marko Rakovic
- Natural History Museum of Belgrade, Belgrade, Serbia
| | - Inês Roque
- MED Mediterranean Institute for Agriculture, Environment and Development, Laboratory of Ornithology, IIFA, University of Évora, Évora, Portugal
| | - Felipe Siverio
- Canary Islands' Ornithology and Natural History Group (GOHNIC), 38480 Buenavista del Norte, Tenerife, Canary Islands, Spain
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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