1
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Bojar AV, Piotrowska N, Barbu V, Bojar HP, Pawełczyk F, Smeu A, Guja O. Ursus spelaeus (Rosenmüller, 1794) during the MIS 3: new evidence from the Cioclovina Uscată Cave and radiocarbon age overview for the Carpathians. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2024:1-13. [PMID: 39049521 DOI: 10.1080/10256016.2024.2376730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/27/2024] [Indexed: 07/27/2024]
Abstract
Ursus spelaeus, the Late Pleistocene a cave bear is known from numerous accumulations found in the fossil sector of caves situated in the Carpathian and Apuseni Mountains. In this study, we present new radiocarbon data along a profile of the Cioclovina Uscată Cave, which is situated in the South Carpathians. The data suggest that, during the entire Marine Isotope Stage 3 (MIS 3) interval, the cave was serving as a shelter for U. spelaeus, with the oldest dated bone indicating an age of > 47,710 and the youngest one, an age of 31,820 ± 400 years cal BP. Histogram plots of 110 radiocarbon data from different caves of the Carpathian and Apuseni Mountains as Cioclovina Uscată, Peștera (Cave) cu Oase, Peștera Muierii, or Peștera Urșilor, respectively, show a maximum expansion of the cave bear population between 50,000 and 40,000, a decline between 40,000 and 35,000 and a partial recovery from 35,000-30,000 years cal BP. Radiocarbon data of Homo sapiens remains, younger than 35,000 years cal BP, support the fact that H. sapiens accessed the same caves where the cave bear persisted to hibernate. Besides general cool conditions and restricted food sources, the presence of H. sapiens constituted an additional stress factor driving the cave bear to extinction.
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Affiliation(s)
- Ana-Voica Bojar
- Department of Environment and Biodiversity, Salzburg University, Salzburg, Austria
- Study Center of Natural History-Mineralogy, Universalmuseum Joanneum, Graz, Austria
| | - Natalia Piotrowska
- Institute of Physics - CSE / Division of Geochronology and Environmental Isotopes, Gliwice, Poland
| | | | - Hans-Peter Bojar
- Study Center of Natural History-Mineralogy, Universalmuseum Joanneum, Graz, Austria
| | - Fatima Pawełczyk
- Institute of Physics - CSE / Division of Geochronology and Environmental Isotopes, Gliwice, Poland
| | - Andrei Smeu
- Faculty of Geology and Geophysics, University of Bucharest, Bucharest, Romania
| | - Ovidiu Guja
- Societatea Națională de Speologie, Cluj-Napoca, Romania
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2
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Winn JC, Maduna SN, Bester-van der Merwe AE. A comprehensive phylogenomic study unveils evolutionary patterns and challenges in the mitochondrial genomes of Carcharhiniformes: A focus on Triakidae. Genomics 2024; 116:110771. [PMID: 38147941 DOI: 10.1016/j.ygeno.2023.110771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/14/2023] [Accepted: 12/22/2023] [Indexed: 12/28/2023]
Abstract
The complex evolutionary patterns in the mitochondrial genome (mitogenome) of the most species-rich shark order, the Carcharhiniformes (ground sharks) has led to challenges in the phylogenomic reconstruction of the families and genera belonging to the order, particularly the family Triakidae (houndsharks). The current state of Triakidae phylogeny remains controversial, with arguments for both monophyly and paraphyly within the family. We hypothesize that this variability is triggered by the selection of different a priori partitioning schemes to account for site and gene heterogeneity within the mitogenome. Here we used an extensive statistical framework to select the a priori partitioning scheme for inference of the mitochondrial phylogenomic relationships within Carcharhiniformes, tested site heterogeneous CAT + GTR + G4 models and incorporated the multi-species coalescent model (MSCM) into our analyses to account for the influence of gene tree discordance on species tree inference. We included five newly assembled houndshark mitogenomes to increase resolution of Triakidae. During the assembly procedure, we uncovered a 714 bp-duplication in the mitogenome of Galeorhinus galeus. Phylogenetic reconstruction confirmed monophyly within Triakidae and the existence of two distinct clades of the expanded Mustelus genus. The latter alludes to potential evolutionary reversal of reproductive mode from placental to aplacental, suggesting that reproductive mode has played a role in the trajectory of adaptive divergence. These new sequences have the potential to contribute to population genomic investigations, species phylogeography delineation, environmental DNA metabarcoding databases and, ultimately, improved conservation strategies for these ecologically and economically important species.
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Affiliation(s)
- Jessica C Winn
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape 7602, South Africa
| | - Simo N Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway
| | - Aletta E Bester-van der Merwe
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape 7602, South Africa.
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3
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White LC. Shallow sequencing can mislead when evaluating hybridization capture methods. CONSERV GENET RESOUR 2023. [DOI: 10.1007/s12686-023-01298-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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4
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Willey C, Korstanje R. Sequencing and assembling bear genomes: the bare necessities. Front Zool 2022; 19:30. [PMID: 36451195 PMCID: PMC9710173 DOI: 10.1186/s12983-022-00475-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Unique genetic adaptations are present in bears of every species across the world. From (nearly) shutting down important organs during hibernation to preventing harm from lifestyles that could easily cause metabolic diseases in humans, bears may hold the answer to various human ailments. However, only a few of these unique traits are currently being investigated at the molecular level, partly because of the lack of necessary tools. One of these tools is well-annotated genome assemblies from the different, extant bear species. These reference genomes are needed to allow us to identify differences in genetic variants, isoforms, gene expression, and genomic features such as transposons and identify those that are associated with biomedical-relevant traits. In this review we assess the current state of the genome assemblies of the eight different bear species, discuss current gaps, and the future benefits these reference genomes may have in informing human biomedical applications, while at the same time improving bear conservation efforts.
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5
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Robin M, Ferrari G, Akgül G, Münger X, von Seth J, Schuenemann VJ, Dalén L, Grossen C. Ancient mitochondrial and modern whole genomes unravel massive genetic diversity loss during near extinction of Alpine ibex. Mol Ecol 2022; 31:3548-3565. [PMID: 35560856 PMCID: PMC9328357 DOI: 10.1111/mec.16503] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/13/2022] [Accepted: 05/04/2022] [Indexed: 11/27/2022]
Abstract
Population bottlenecks can have dramatic consequences for the health and long-term survival of a species. Understanding of historic population size and standing genetic variation prior to a contraction allows estimating the impact of a bottleneck on the species genetic diversity. Although historic population sizes can be modelled based on extant genomics, uncertainty is high for the last 10-20 millenia. Hence, integrating ancient genomes provides a powerful complement to retrace the evolution of genetic diversity through population fluctuations. Here, we recover 15 high-quality mitogenomes of the once nearly extinct Alpine ibex spanning 8601 BP to 1919 CE and combine these with 60 published modern whole genomes. Coalescent demography simulations based on modern whole genomes indicate population fluctuations coinciding with the last major glaciation period. Using our ancient and historic mitogenomes, we investigate the more recent demographic history of the species and show that mitochondrial haplotype diversity was reduced to a fifth of the pre-bottleneck diversity with several highly differentiated mitochondrial lineages having co-existed historically. The main collapse of mitochondrial diversity coincides with elevated human population growth during the last 1-2 kya. After recovery, one lineage was spread and nearly fixed across the Alps due to recolonization efforts. Our study highlights that a combined approach integrating genomic data of ancient, historic and extant populations unravels major long-term population fluctuations from the emergence of a species through its near extinction up to the recent past.
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Affiliation(s)
- Mathieu Robin
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland.,Institute of Evolutionary Medicine, University of Zurich, Zürich, Switzerland
| | - Giada Ferrari
- Institute of Evolutionary Medicine, University of Zurich, Zürich, Switzerland
| | - Gülfirde Akgül
- Institute of Evolutionary Medicine, University of Zurich, Zürich, Switzerland
| | - Xenia Münger
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Johanna von Seth
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Christine Grossen
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
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6
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Dussex N, Bergfeldt N, de Anca Prado V, Dehasque M, Díez-Del-Molino D, Ersmark E, Kanellidou F, Larsson P, Lemež Š, Lord E, Mármol-Sánchez E, Meleg IN, Måsviken J, Naidoo T, Studerus J, Vicente M, von Seth J, Götherström A, Dalén L, Heintzman PD. Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics. Proc Biol Sci 2021; 288:20211252. [PMID: 34428961 PMCID: PMC8385357 DOI: 10.1098/rspb.2021.1252] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.
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Affiliation(s)
- Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Nora Bergfeldt
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Marianne Dehasque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Erik Ersmark
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Foteini Kanellidou
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Petter Larsson
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Špela Lemež
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Emilio Mármol-Sánchez
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ioana N Meleg
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,'Emil Racoviță' Institute of Speleology of the Romanian Academy, Calea 13 Septembrie, nr. 13, 050711, Sector 5, Bucharest, Romania.,Emil. G. Racoviță Institute, Babeș-Bolyai University, Clinicilor 5-7, 400006 Cluj-Napoca, Romania
| | - Johannes Måsviken
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Thijessen Naidoo
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Ancient DNA Unit, SciLifeLab, Stockholm and Uppsala, Sweden
| | - Jovanka Studerus
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Mário Vicente
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Peter D Heintzman
- The Arctic University Museum of Norway, The Arctic University of Norway, 9037 Tromsø, Norway
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7
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Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches. DIVERSITY 2021. [DOI: 10.3390/d13080370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.
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8
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Bortolini E, Pagani L, Oxilia G, Posth C, Fontana F, Badino F, Saupe T, Montinaro F, Margaritora D, Romandini M, Lugli F, Papini A, Boggioni M, Perrini N, Oxilia A, Cigliano RA, Barcelona R, Visentin D, Fasser N, Arrighi S, Figus C, Marciani G, Silvestrini S, Bernardini F, Menghi Sartorio JC, Fiorenza L, Cecchi JM, Tuniz C, Kivisild T, Gianfrancesco F, Peresani M, Scheib CL, Talamo S, D'Esposito M, Benazzi S. Early Alpine occupation backdates westward human migration in Late Glacial Europe. Curr Biol 2021; 31:2484-2493.e7. [PMID: 33887180 DOI: 10.1016/j.cub.2021.03.078] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/07/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023]
Abstract
Before the end of the Last Glacial Maximum (LGM, ∼16.5 ka ago)1 set in motion major shifts in human culture and population structure,2 a consistent change in lithic technology, material culture, settlement pattern, and adaptive strategies is recorded in Southern Europe at ∼18-17 ka ago. In this time frame, the landscape of Northeastern Italy changed considerably, and the retreat of glaciers allowed hunter-gatherers to gradually recolonize the Alps.3-6 Change within this renewed cultural frame (i.e., during the Late Epigravettian phase) is currently associated with migrations favored by warmer climate linked to the Bølling-Allerød onset (14.7 ka ago),7-11 which replaced earlier genetic lineages with ancestry found in an individual who lived ∼14 ka ago at Riparo Villabruna, Italy, and shared among different contexts (Villabruna Cluster).9 Nevertheless, these dynamics and their chronology are still far from being disentangled due to fragmentary evidence for long-distance interactions across Europe.12 Here, we generate new genomic data from a human mandible uncovered at Riparo Tagliente (Veneto, Italy), which we directly dated to 16,980-16,510 cal BP (2σ). This individual, affected by focal osseous dysplasia, is genetically affine to the Villabruna Cluster. Our results therefore backdate by at least 3 ka the diffusion in Southern Europe of a genetic component linked to Balkan/Anatolian refugia, previously believed to have spread during the later Bølling/Allerød event. In light of the new genetic evidence, this population replacement chronologically coincides with the very emergence of major cultural transitions in Southern and Western Europe.
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Affiliation(s)
- Eugenio Bortolini
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy; CaSEs (Culture and Socio-Ecological Dynamics) Department of Humanities, Universitat Pompeu Fabra, Ramon Trias Fargas, 25-27, 08005 Barcelona, Spain.
| | - Luca Pagani
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy; Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b 51010 Tartu, Estonia.
| | - Gregorio Oxilia
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy.
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany
| | - Federica Fontana
- Department of Humanities - Section of Prehistoric and Anthropological Sciences, University of Ferrara, Corso Ercole I d'Este 32, 44121 Ferrara, Italy
| | - Federica Badino
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy; Research Group on Vegetation, Climate and Human Stratigraphy, Lab of Palynology and Palaeoecology, CNR - Institute of Environmental Geology and Geoengineering (IGAG), 20126 Milano, Italy
| | - Tina Saupe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b 51010 Tartu, Estonia
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b 51010 Tartu, Estonia
| | - Davide Margaritora
- Department of Humanities - Section of Prehistoric and Anthropological Sciences, University of Ferrara, Corso Ercole I d'Este 32, 44121 Ferrara, Italy
| | - Matteo Romandini
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy
| | - Federico Lugli
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy
| | - Andrea Papini
- Dentist surgeon, via Walter Tobagi 35, 59100 Prato, Italy
| | - Marco Boggioni
- Dentist surgeon, via D'Andrade 34/207, 16154 Genova Sestri Ponente, Italy
| | - Nicola Perrini
- Dentist surgeon, Centro di Odontoiatria e Stomatologia, Via Luca Signorelli, 5, 51100 Pistoia PT, Italy
| | - Antonio Oxilia
- General surgeon, via Marcantonio Della Torre, 7, 37131 Verona, Italy
| | | | - Rosa Barcelona
- Sequentia Biotech, Calle Comte D'Urgell 240, 08036 Barcelona, Spain; Institute of Genetics and Biophysics "Adriano Buzzati-Traverso," National Research Council of Italy, Via P.Castellino 111, 80131 Naples, Italy; Departamento de Matemáticas, Escuela Técnica Superior de Ingeniería Industrial de Barcelona (ETSEIB), Universitat Politècnica de Catalunya (UPC), Diagonal 647, 08028 Barcelona, Spain
| | - Davide Visentin
- Archaeology of Social Dynamics, Institució Milà i Fontanals, Spanish National Research Council (IMF-CSIC), C/Egipcíaques 15, 08001 Barcelona, Spain
| | - Nicolò Fasser
- Department of Humanities - Section of Prehistoric and Anthropological Sciences, University of Ferrara, Corso Ercole I d'Este 32, 44121 Ferrara, Italy
| | - Simona Arrighi
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy
| | - Carla Figus
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy
| | - Giulia Marciani
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy
| | - Sara Silvestrini
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy
| | - Federico Bernardini
- Department of Humanities, Università Ca' Foscari Venezia, Dorsoduro, 3484/D, 30123 Venezia, Italy; Multidisciplinary Laboratory, The "Abdus Salam" International Centre for Theoretical Physics (ICTP), Strada Costiera, 11 - 34151 Trieste, Italy
| | - Jessica C Menghi Sartorio
- Department of Humanities - Section of Prehistoric and Anthropological Sciences, University of Ferrara, Corso Ercole I d'Este 32, 44121 Ferrara, Italy
| | - Luca Fiorenza
- Monash Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Earth Sciences, University of New England, Armidale, NSW 2351, Australia
| | - Jacopo Moggi Cecchi
- Department of Biology, University of Florence, Via del Proconsolo, 12, Firenze 50122, Italy
| | - Claudio Tuniz
- Multidisciplinary Laboratory, The "Abdus Salam" International Centre for Theoretical Physics (ICTP), Strada Costiera, 11 - 34151 Trieste, Italy; Centre for Archaeological Science, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b 51010 Tartu, Estonia; Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Fernando Gianfrancesco
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso," National Research Council of Italy, Via P.Castellino 111, 80131 Naples, Italy
| | - Marco Peresani
- Department of Humanities - Section of Prehistoric and Anthropological Sciences, University of Ferrara, Corso Ercole I d'Este 32, 44121 Ferrara, Italy
| | - Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b 51010 Tartu, Estonia
| | - Sahra Talamo
- Department of Chemistry "G. Ciamician," University of Bologna, Via Selmi, 2, 40126 Bologna, Italy; Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Maurizio D'Esposito
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso," National Research Council of Italy, Via P.Castellino 111, 80131 Naples, Italy
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy; Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution, Deutscher Platz 6, 04103 Leipzig, Germany
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9
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Rey-Iglesia A, Lister AM, Campos PF, Brace S, Mattiangeli V, Daly KG, Teasdale MD, Bradley DG, Barnes I, Hansen AJ. Exploring the phylogeography and population dynamics of the giant deer ( Megaloceros giganteus) using Late Quaternary mitogenomes. Proc Biol Sci 2021; 288:20201864. [PMID: 33977786 PMCID: PMC8114472 DOI: 10.1098/rspb.2020.1864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 04/15/2021] [Indexed: 12/20/2022] Open
Abstract
Late Quaternary climatic fluctuations in the Northern Hemisphere had drastic effects on large mammal species, leading to the extinction of a substantial number of them. The giant deer (Megaloceros giganteus) was one of the species that became extinct in the Holocene, around 7660 calendar years before present. In the Late Pleistocene, the species ranged from western Europe to central Asia. However, during the Holocene, its range contracted to eastern Europe and western Siberia, where the last populations of the species occurred. Here, we generated 35 Late Pleistocene and Holocene giant deer mitogenomes to explore the genetics of the demise of this iconic species. Bayesian phylogenetic analyses of the mitogenomes suggested five main clades for the species: three pre-Last Glacial Maximum clades that did not appear in the post-Last Glacial Maximum genetic pool, and two clades that showed continuity into the Holocene. Our study also identified a decrease in genetic diversity starting in Marine Isotope Stage 3 and accelerating during the Last Glacial Maximum. This reduction in genetic diversity during the Last Glacial Maximum, coupled with a major contraction of fossil occurrences, suggests that climate was a major driver in the dynamics of the giant deer.
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Affiliation(s)
- Alba Rey-Iglesia
- Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen, Østervoldgade 5-7, 1350 Copenhagen, Denmark
| | - Adrian M. Lister
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Paula F. Campos
- Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen, Østervoldgade 5-7, 1350 Copenhagen, Denmark
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, 4450-208 Matosinhos, Portugal
| | - Selina Brace
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin Dublin 2, Ireland
| | - Kevin G. Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin Dublin 2, Ireland
| | - Matthew D. Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin Dublin 2, Ireland
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin Dublin 2, Ireland
| | - Ian Barnes
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Anders J. Hansen
- Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen, Østervoldgade 5-7, 1350 Copenhagen, Denmark
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Barlow A, Paijmans JLA, Alberti F, Gasparyan B, Bar-Oz G, Pinhasi R, Foronova I, Puzachenko AY, Pacher M, Dalén L, Baryshnikov G, Hofreiter M. Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears. Curr Biol 2021; 31:1771-1779.e7. [PMID: 33592193 DOI: 10.1016/j.cub.2021.01.073] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 10/19/2020] [Accepted: 01/21/2021] [Indexed: 11/18/2022]
Abstract
Palaeogenomes provide the potential to study evolutionary processes in real time, but this potential is limited by our ability to recover genetic data over extended timescales.1 As a consequence, most studies so far have focused on samples of Late Pleistocene or Holocene age, which covers only a small part of the history of many clades and species. Here, we report the recovery of a low coverage palaeogenome from the petrous bone of a ∼360,000 year old cave bear from Kudaro 1 cave in the Caucasus Mountains. Analysis of this genome alongside those of several Late Pleistocene cave bears reveals widespread mito-nuclear discordance in this group. Using the time interval between Middle and Late Pleistocene cave bear genomes, we directly estimate ursid nuclear and mitochondrial substitution rates to calibrate their respective phylogenies. This reveals post-divergence mitochondrial transfer as the dominant factor explaining their mito-nuclear discordance. Interestingly, these transfer events were not accompanied by large-scale nuclear introgression. However, we do detect additional instances of nuclear admixture among other cave bear lineages, and between cave bears and brown bears, which are not associated with mitochondrial exchange. Genomic data obtained from the Middle Pleistocene cave bear petrous bone has thus facilitated a revised evolutionary history of this extinct megafaunal group. Moreover, it suggests that petrous bones may provide a means of extending both the magnitude and time depth of palaeogenome retrieval over substantial portions of the evolutionary histories of many mammalian clades.
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Affiliation(s)
- Axel Barlow
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK; Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany.
| | - Johanna L A Paijmans
- School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Federica Alberti
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, 0025, RA, Yerevan, 15 Charents st., Armenia
| | - Guy Bar-Oz
- The Zinman Institute of Archaeology, University of Haifa, 199 Aba-Hushi Avenue, Haifa, Israel 3498838
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Irina Foronova
- V.S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, 3, Ac. Koptyuga ave., Novosibirsk, Russia 630090
| | - Andrey Y Puzachenko
- Institute of Geography, Russian Academy of Sciences, Staromonetnyy Pereulok, 29, Moscow, Russia 119017
| | - Martina Pacher
- Naturmuseum St. Gallen, Rorschacher Strasse 263, CH-9016 St. Gallen, Switzerland
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Frescativägen 54, 114 18 Stockholm, Sweden
| | - Gennady Baryshnikov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Naberezhnaya 1, 199034 St. Petersburg, Russia
| | - Michael Hofreiter
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
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11
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Cost-effective straightforward method for captured whole mitogenome sequencing of ancient DNA. Forensic Sci Int 2020; 319:110638. [PMID: 33340848 DOI: 10.1016/j.forsciint.2020.110638] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/28/2020] [Accepted: 11/29/2020] [Indexed: 11/21/2022]
Abstract
Working with mitochondrial DNA from highly degraded samples is challenging. We present a whole mitogenome Illumina-based sequencing method suitable for highly degraded samples. The method makes use of double-stranded library preparation with hybridization-based target enrichment. The aim of the study was to implement a new user-friendly method for analysing many ancient DNA samples at low cost. The method combines the Swift 2S™ Turbo library preparation kit and xGen® panel for mitogenome enrichment. Swift allows to use low input of aDNA and own adapters and primers, handles inhibitors well, and has only two purification steps. xGen is straightforward to use and is able to leverage already pooled libraries. Given the ancient DNA is more challenging to work with, the protocol was developed with several improvements, especially multiplying DNA input in case of low concentration DNA extractions followed by AMPure® beads size selection and real-time pre-capture PCR monitoring in order to avoid cycle-optimization step. Nine out of eleven analysed samples successfully retrieved mitogenomes. Hence, our method provides an effective analysis of whole mtDNA, and has proven to be fast, cost-effective, straightforward, with utilisation in population-wide research of burial sites.
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Lucena-Perez M, Marmesat E, Kleinman-Ruiz D, Martínez-Cruz B, Węcek K, Saveljev AP, Seryodkin IV, Okhlopkov I, Dvornikov MG, Ozolins J, Galsandorj N, Paunovic M, Ratkiewicz M, Schmidt K, Godoy JA. Genomic patterns in the widespread Eurasian lynx shaped by Late Quaternary climatic fluctuations and anthropogenic impacts. Mol Ecol 2020; 29:812-828. [PMID: 31995648 PMCID: PMC7064982 DOI: 10.1111/mec.15366] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 12/27/2019] [Accepted: 01/16/2020] [Indexed: 12/28/2022]
Abstract
Disentangling the contribution of long-term evolutionary processes and recent anthropogenic impacts to current genetic patterns of wildlife species is key to assessing genetic risks and designing conservation strategies. Here, we used 80 whole nuclear genomes and 96 mitogenomes from populations of the Eurasian lynx covering a range of conservation statuses, climatic zones and subspecies across Eurasia to infer the demographic history, reconstruct genetic patterns, and discuss the influence of long-term isolation and/or more recent human-driven changes. Our results show that Eurasian lynx populations shared a common history until 100,000 years ago, when Asian and European populations started to diverge and both entered a period of continuous and widespread decline, with western populations, except Kirov, maintaining lower effective sizes than eastern populations. Population declines and increased isolation in more recent times probably drove the genetic differentiation between geographically and ecologically close westernmost European populations. By contrast, and despite the wide range of habitats covered, populations are quite homogeneous genetically across the Asian range, showing a pattern of isolation by distance and providing little genetic support for the several proposed subspecies. Mitogenomic and nuclear divergences and population declines starting during the Late Pleistocene can be mostly attributed to climatic fluctuations and early human influence, but the widespread and sustained decline since the Holocene is more probably the consequence of anthropogenic impacts which intensified in recent centuries, especially in western Europe. Genetic erosion in isolated European populations and lack of evidence for long-term isolation argue for the restoration of lost population connectivity.
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Affiliation(s)
- Maria Lucena-Perez
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Seville, Spain
| | - Elena Marmesat
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Seville, Spain
| | - Daniel Kleinman-Ruiz
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Seville, Spain
| | - Begoña Martínez-Cruz
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Karolina Węcek
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Alexander P Saveljev
- Department of Animal Ecology, Russian Research Institute of Game Management and Fur Farming, Kirov, Russia.,Biological Faculty of Moscow State University, Moscow, Russia
| | - Ivan V Seryodkin
- Laboratory of Ecology and Conservation of Animals, Pacific Institute of Geography of Far East Branch of Russian Academy of Sciences, Vladivostok, Russia.,Far Eastern Federal University, Vladivostok, Russia
| | - Innokentiy Okhlopkov
- Institute for Biological Problems of Cryolithozone, Siberian Division of the Russian Academy of Sciences, Yakutsk, Russia
| | - Mikhail G Dvornikov
- Department of Hunting Resources, Russian Research Institute of Game Management and Fur Farming, Kirov, Russia
| | - Janis Ozolins
- Department of Hunting and Wildlife Management, Latvijas Valsts mežzinātnes institūts "Silava", Salaspils, Latvia
| | - Naranbaatar Galsandorj
- Institute of General and Experimental Biology, Mongolian Academy of Science, Ulaanbaatar, Mongolia
| | | | | | - Krzysztof Schmidt
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - José A Godoy
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), Seville, Spain
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