4.6 Review

The Small and the Dead: A Review of Ancient DNA Studies Analysing Micromammal Species

期刊

GENES
卷 8, 期 11, 页码 -

出版社

MDPI
DOI: 10.3390/genes8110312

关键词

ancient DNA; small mammals; micromammals; palaeogenetics

向作者/读者索取更多资源

The field of ancient DNA (aDNA) has recently been in a state of exponential growth, largely driven by the uptake of Next Generation Sequencing (NGS) techniques. Much of this work has focused on the mammalian megafauna and ancient humans, with comparatively less studies looking at micromammal fauna, despite the potential of these species in testing evolutionary, environmental and taxonomic theories. Several factors make micromammal fauna ideally suited for aDNA extraction and sequencing. Micromammal subfossil assemblages often include the large number of individuals appropriate for population level analyses, and, furthermore, the assemblages are frequently found in cave sites where the constant temperature and sheltered environment provide favourable conditions for DNA preservation. This review looks at studies that include the use of aDNA in molecular analysis of micromammal fauna, in order to examine the wide array of questions that can be answered in the study of small mammals using new palaeogenetic techniques. This study highlights the bias in current aDNA studies and assesses the future use of aDNA as a tool for the study of micromammal fauna.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.6
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Article Multidisciplinary Sciences

Radiocarbon chronology and environmental context of Last Glacial Maximum human occupation in Switzerland

Hazel Reade, Jennifer A. Tripp, Sophy Charlton, Sonja Grimm, Kerry L. Sayle, Alex Fensome, Thomas F. G. Higham, Ian Barnes, Rhiannon E. Stevens

SCIENTIFIC REPORTS (2020)

Article Biochemistry & Molecular Biology

Ancient DNA Suggests Single Colonization and Within-Archipelago Diversification of Caribbean Caviomorph Rodents

Roseina Woods, Ian Barnes, Selina Brace, Samuel T. Turvey

Summary: This study uses ancient DNA techniques to show that Caribbean caviomorphs form a well-supported monophyletic group, with their remarkable morphological and ecological variation resulting from evolutionary radiation post a single Early Miocene colonization event. The living and extinct caviomorphs in the Caribbean are part of a biologically remarkable subfamily within the living Neotropical family Echimyidae, representing an important example of insular mammalian adaptive radiation where ancestral-type characteristics coexisted with taxa occupying novel island niches. The diversification of Caribbean caviomorphs is associated with the largest insular body mass increase observed in rodents and possibly any mammal lineage.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Multidisciplinary Sciences

Million-year-old DNA sheds light on the genomic history of mammoths

Tom van der Valk, Patricia Pecnerova, David Diez-del-Molino, Anders Bergstrom, Jonas Oppenheimer, Stefanie Hartmann, Georgios Xenikoudakis, Jessica A. Thomas, Marianne Dehasque, Ekin Saglican, Fatma Rabia Fidan, Ian Barnes, Shanlin Liu, Mehmet Somel, Peter D. Heintzman, Pavel Nikolskiy, Beth Shapiro, Pontus Skoglund, Michael Hofreiter, Adrian M. Lister, Anders Gotherstrom, Love Dalen

Summary: This study reveals the presence of two distinct mammoth lineages in eastern Siberia during the Early Pleistocene, with one lineage giving rise to the woolly mammoth and another representing an unrecognized lineage ancestral to the first mammoths to colonize North America. Additionally, the study shows that the Columbian mammoth of North America can trace its ancestry back to a hybridization event between these two lineages during the Middle Pleistocene, with roughly equal admixture proportions. Moreover, the majority of protein-coding changes associated with cold adaptation in woolly mammoths were found to be present as early as one million years ago.

NATURE (2021)

Article Biology

Exploring the phylogeography and population dynamics of the giant deer (Megaloceros giganteus) using Late Quaternary mitogenomes

Alba Rey-Iglesia, Adrian M. Lister, Paula F. Campos, Selina Brace, Valeria Mattiangeli, Kevin G. Daly, Matthew D. Teasdale, Daniel G. Bradley, Ian Barnes, Anders J. Hansen

Summary: Late Quaternary climatic fluctuations had significant impacts on the extinction of large mammal species, including the giant deer. Genetic analyses of mitogenomes revealed five main clades for the species, with a decrease in genetic diversity during the Last Glacial Maximum. This reduction, along with a contraction of fossil occurrences, suggests that climate played a major role in the extinction of the giant deer.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2021)

Article Multidisciplinary Sciences

Large-scale migration into Britain during the Middle to Late Bronze Age

Nick Patterson, Michael Isakov, Thomas Booth, Lindsey Buster, Claire-Elise Fischer, Inigo Olalde, Harald Ringbauer, Ali Akbari, Olivia Cheronet, Madeleine Bleasdale, Nicole Adamski, Eveline Altena, Rebecca Bernardos, Selina Brace, Nasreen Broomandkhoshbacht, Kimberly Callan, Francesca Candilio, Brendan Culleton, Elizabeth Curtis, Lea Demetz, Kellie Sara Duffett Carlson, Ceiridwen J. Edwards, Daniel M. Fernandes, M. George B. Foody, Suzanne Freilich, Helen Goodchild, Aisling Kearns, Ann Marie Lawson, Iosif Lazaridis, Matthew Mah, Swapan Mallick, Kirsten Mandl, Adam Micco, Megan Michel, Guillermo Bravo Morante, Jonas Oppenheimer, Kadir Toykan Ozdogan, Lijun Qiu, Constanze Schattke, Kristin Stewardson, J. Noah Workman, Fatma Zalzala, Zhao Zhang, Bibiana Agusti, Tim Allen, Katalin Almassy, Luc Amkreutz, Abigail Ash, Christele Baillif-Ducros, Alistair Barclay, Laszlo Bartosiewicz, Katherine Baxter, Zsolt Bernert, Jan Blazek, Mario Bodruzic, Philippe Boissinot, Clive Bonsall, Pippa Bradley, Marcus Brittain, Alison Brookes, Fraser Brown, Lisa Brown, Richard Brunning, Chelsea Budd, Josip Burmaz, Sylvain Canet, Silvia Carnicero-Caceres, Morana Causevic-Bully, Andrew Chamberlain, Sebastien Chauvin, Sharon Clough, Natalija Condic, Alfredo Coppa, Oliver Craig, Matija Cresnar, Vicki Cummings, Szabolcs Czifra, Alzbeta Danielisova, Robin Daniels, Alex Davies, Philip de Jersey, Jody Deacon, Csilla Deminger, Peter W. Ditchfield, Marko Dizdar, Miroslav Dobes, Miluse Dobisikova, Laszlo Domboroczki, Gail Drinkall, Ana Dukic, Michal Ernee, Christopher Evans, Jane Evans, Manuel Fernandez-Gotz, Slavica Filipovic, Andrew Fitzpatrick, Harry Fokkens, Chris Fowler, Allison Fox, Zsolt Gallina, Michelle Gamble, Manuel R. Gonzalez Morales, Borja Gonzalez-Rabanal, Adrian Green, Katalin Gyenesei, Diederick Habermehl, Tamas Hajdu, Derek Hamilton, James Harris, Chris Hayden, Joep Hendriks, Benedicte Hernu, Gill Hey, Milan Hornak, Gabor Ilon, Eszter Istvanovits, Andy M. Jones, Martina Blecic Kavur, Kevin Kazek, Robert A. Kenyon, Amal Khreisheh, Viktoria Kiss, Jos Kleijne, Mark Knight, Lisette M. Kootker, Peter F. Kovacs, Anita Kozubova, Gabriella Kulcsar, Valeria Kulcsar, Christophe Le Pennec, Michael Legge, Matt Leivers, Louise Loe, Olalla Lopez-Costas, Tom Lord, Dzeni Los, James Lyall, Ana B. Marin-Arroyo, Philip Mason, Damir Matosevic, Andy Maxted, Lauren McIntyre, Jacqueline McKinley, Kathleen McSweeney, Bernard Meijlink, Balazs G. Mende, Marko Mendusic, Milan Metlicka, Sophie Meyer, Kristina Mihovilic, Lidija Milasinovic, Steve Minnitt, Joanna Moore, Geoff Morley, Graham Mullan, Margareta Musilova, Benjamin Neil, Rebecca Nicholls, Mario Novak, Maria Pala, Martin Papworth, Cecile Paresys, Ricky Patten, Domagoj Perkic, Krisztina Pesti, Alba Petit, Katarina Petrisakova, Coline Pichon, Catriona Pickard, Zoltan Pilling, T. Douglas Price, Sinisa Radovic, Rebecca Redfern, Branislav Resutik, Daniel T. Rhodes, Martin B. Richards, Amy Roberts, Jean Roefstra, Pavel Sankot, Alena Sefcakova, Alison Sheridan, Sabine Skae, Miroslava Smolikova, Krisztina Somogyi, Agnes Somogyvari, Mark Stephens, Geza Szabo, Anna Szecsenyi-Nagy, Tamas Szeniczey, Jonathan Tabor, Karoly Tanko, Clenis Tavarez Maria, Rachel Terry, Biba Terzan, Maria Teschler-Nicola, Jesus F. Torres-Martinez, Julien Trapp, Ross Turle, Ferenc Ujvari, Menno van der Heiden, Petr Veleminsky, Barbara Veselka, Zdenek Vytlacil, Clive Waddington, Paula Ware, Paul Wilkinson, Linda Wilson, Rob Wiseman, Eilidh Young, Josko Zaninovic, Andrej Zitnan, Carles Lalueza-Fox, Peter de Knijff, Ian Barnes, Peter Halkon, Mark G. Thomas, Douglas J. Kennett, Barry Cunliffe, Malcolm Lillie, Nadin Rohland, Ron Pinhasi, Ian Armit, David Reich

Summary: Present-day people from England and Wales have more ancestry derived from early European farmers, potentially due to early migration patterns and cultural exchanges. The utilization of dairy products differed qualitatively in Britain compared to continental Europe during the Iron Age.

NATURE (2022)

Review Ecology

Ancient and historical DNA in conservation policy

Evelyn L. Jensen, David Diez-del-Molino, M. Thomas P. Gilbert, Laura D. Bertola, Filipa Borges, Vlatka Cubric-Curik, Miguel de Navascues, Peter Frandsen, Myriam Heuertz, Christina Hvilsom, Belen Jimenez-Mena, Antti Miettinen, Markus Moest, Patricia Pecnerova, Ian Barnes, Cristiano Vernesi

Summary: Genetic diversity, including ancient and historical DNA, plays a crucial role in biodiversity conservation. However, it has not been adequately incorporated into conservation policies and regulations. Utilizing genetic information from ancient and historical specimens can help resolve key conservation issues and assist countries in meeting their obligations under the Convention on Biological Diversity (CBD).

TRENDS IN ECOLOGY & EVOLUTION (2022)

Article Multidisciplinary Sciences

Grey wolf genomic history reveals a dual ancestry of dogs

Anders Bergstrom, David W. G. Stanton, Ulrike H. Taron, Laurent Frantz, Mikkel-Holger S. Sinding, Erik Ersmark, Saskia Pfrengle, Molly Cassatt-Johnstone, Ophelie Lebrasseur, Linus Girdland-Flink, Daniel M. Fernandes, Morgane Ollivier, Leo Speidel, Shyam Gopalakrishnan, Michael V. Westbury, Jazmin Ramos-Madrigal, Tatiana R. Feuerborn, Ella Reiter, Joscha Gretzinger, Susanne C. Muenzel, Pooja Swali, Nicholas J. Conard, Christian Caroe, James Haile, Anna Linderholm, Semyon Androsov, Ian Barnes, Chris Baumann, Norbert Benecke, Herve Bocherens, Selina Brace, Ruth F. Carden, Dorothee G. Drucker, Sergey Fedorov, Mihaly Gasparik, Mietje Germonpre, Semyon Grigoriev, Pam Groves, Stefan T. Hertwig, Varvara V. Ivanova, Luc Janssens, Richard P. Jennings, Aleksei K. Kasparov, Irina V. Kirillova, Islam Kurmaniyazov, Yaroslav V. Kuzmin, Pavel A. Kosintsev, Martina Laznickova-Galetova, Charlotte Leduc, Pavel Nikolskiy, Marc Nussbaumer, Coilin O'Drisceoil, Ludovic Orlando, Alan Outram, Elena Y. Pavlova, Angela R. Perri, Malgorzata Pilot, Vladimir V. Pitulko, Valerii V. Plotnikov, Albert V. Protopopov, Andre Rehazek, Mikhail Sablin, Andaine Seguin-Orlando, Jan Stora, Christian Verjux, Victor F. Zaibert, Grant Zazula, Philippe Crombe, Anders J. Hansen, Eske Willerslev, Jennifer A. Leonard, Anders Gotherstrom, Ron Pinhasi, Verena J. Schuenemann, Michael Hofreiter, M. Thomas P. Gilbert, Beth Shapiro, Greger Larson, Johannes Krause, Love Dalen, Pontus Skoglund

Summary: This article analyzes ancient wolf genomes and finds that wolf populations were highly connected in the late Pleistocene, suggesting a complex history of wolf domestication. Dogs are overall more closely related to ancient wolves from eastern Eurasia, but dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves.

NATURE (2022)

Article Biochemistry & Molecular Biology

Genomes from a medieval mass burial show Ashkenazi-associated hereditary diseases pre-date the 12th century

Selina Brace, Yoan Diekmann, Thomas Booth, Ruairidh Macleod, Adrian Timpson, Will Stephen, Giles Emery, Sophie Cabot, Mark G. Thomas, Ian Barnes

Summary: The genome sequences of six individuals excavated from a medieval well in Norwich, UK, reveal that four individuals were closely related and all six had strong genetic affinities with modem Ashkenazi Jews. The findings provide new insights into a historically significant crime, Ashkenazi population history, and the origins of genetic diseases associated with modern Jewish populations.

CURRENT BIOLOGY (2022)

Article Multidisciplinary Sciences

The Anglo-Saxon migration and the formation of the early English gene pool

Joscha Gretzinger, Duncan Sayer, Pierre Justeau, Eveline Altena, Maria Pala, Katharina Dulias, Ceiridwen J. Edwards, Susanne Jodoin, Laura Lacher, Susanna Sabin, Ashild J. Vagene, Wolfgang Haak, S. Sunna Ebenesersdottir, Kristjan H. S. Moore, Rita Radzeviciute, Kara Schmidt, Selina Brace, Martina Abenhus Bager, Nick Patterson, Luka Papac, Nasreen Broomandkhoshbacht, Kimberly Callan, Lora Iliev, Ann Marie Lawson, Megan Michel, Kristin Stewardson, Fatma Zalzala, Nadin Rohland, Stefanie Kappelhoff-Beckmann, Frank Both, Daniel Winger, Daniel Neumann, Lars Saalow, Stefan Krabath, Sophie Beckett, Melanie Van Twest, Neil Faulkner, Chris Read, Tabatha Barton, Joanna Caruth, John Hines, Ben Krause-Kyora, Ursula Warnke, Verena J. Schuenemann, Ian Barnes, Hanna Dahlstrom, Jane Jark Clausen, Andrew Richardson, Elizabeth Popescu, Natasha Dodwell, Stuart Ladd, Tom Phillips, Richard Mortimer, Faye Sayer, Diana Swales, Allison Stewart, Dominic Powlesland, Robert Kenyon, Lilian Ladle, Christina Peek, Silke Grefen-Peters, Paola Ponce, Robin Daniels, Cecily Spall, Jennifer Woolcock, Andy M. Jones, Amy Roberts, Robert Symmons, Anooshka C. Rawden, Alan Cooper, Kirsten Bos, Tom Booth, Hannes Schroeder, Mark G. Thomas, Agnar Helgason, Martin B. Richards, David Reich, Johannes Krause, Stephan Schiffels

Summary: The study of ancient DNA from medieval northwestern Europeans and archaeological data reveals a significant migration of continental northern European ancestry into early medieval England, with substantial regional variation and heterogeneity. Women with immigrant ancestry were more likely to have grave goods, while men with weapons may not have immigrant ancestry. Subsequent demographic events in present-day Britain reduced the fraction of continental northern European ancestry while introducing additional ancestry components, including substantial southwestern European ancestry related to Iron Age France.

NATURE (2022)

Article Ecology

First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing

Victoria E. Mullin, William Stephen, Andres N. Arce, Will Nash, Calum Raine, David G. Notton, Ashleigh Whiffin, Vladimir Blagderov, Karim Gharbi, James Hogan, Tony Hunter, Naomi Irish, Simon Jackson, Steve Judd, Chris Watkins, Wilfried Haerty, Jeff Ollerton, Selina Brace, Richard J. Gill, Ian Barnes

Summary: Insect declines have significant ecological and economic ramifications, but the genomic impact of these losses is poorly understood. This study demonstrates how Next-Generation Sequencing methods can be used to analyze the preservation of DNA in museum specimens and provides insights into the rate of DNA decay over time. The findings show that historical insects can serve as valuable sources of genetic information, as long as the degraded nature of DNA is accounted for.

METHODS IN ECOLOGY AND EVOLUTION (2023)

Article Ecology

Dual ancestries and ecologies of the Late Glacial Palaeolithic in Britain

Sophy Charlton, Selina Brace, Mateja Hajdinjak, Rebecca Kearney, Thomas Booth, Hazel Reade, Jennifer A. Tripp, Kerry L. Sayle, Sonja B. Grimm, Silvia M. Bello, Elizabeth A. Walker, Alexandre Gilardet, Philip East, Isabelle Glocke, Greger Larson, Tom Higham, Chris Stringer, Pontus Skoglund, Ian Barnes, Rhiannon E. Stevens

Summary: Research reveals diverse origins and ways of life among inhabitants of late Pleistocene Britain, as individuals from different archaeological sites exhibit distinct genetic ancestries, diets, and ecologies.

NATURE ECOLOGY & EVOLUTION (2022)

Article Biotechnology & Applied Microbiology

Inferring biological kinship in ancient datasets: comparing the response of ancient DNA-specific software packages to low coverage data

William A. Marsh, Selina Brace, Ian Barnes

Summary: The use of archaeogenetic techniques, in combination with traditional methods, allows for improved interpretation of burial practices, cultural behaviors, and societal stratification in ancient societies. However, questions remain regarding the accuracy of these techniques, especially when it comes to low coverage datasets obtained from degraded ancient material. A study comparing six commonly used kinship identification software methods revealed differences in performance, emphasizing the importance of applying multiple methods for authentication of kin relationships in ancient material.

BMC GENOMICS (2023)

Article Multidisciplinary Sciences

Ancient human DNA recovered from a Palaeolithic pendant

Elena Essel, Elena I. Zavala, Ellen Schulz-Kornas, Maxim B. Kozlikin, Helen Fewlass, Benjamin Vernot, Michael V. Shunkov, Anatoly P. Derevianko, Katerina Douka, Ian Barnes, Marie-Cecile Soulier, Anna Schmidt, Merlin Szymanski, Tsenka Tsanova, Nikolay Sirakov, Elena Endarova, Shannon P. McPherron, Jean-Jacques Hublin, Janet Kelso, Svante Paeaebo, Mateja Hajdinjak, Marie Soressi, Matthias Meyer

Summary: Artefacts made from stones, bones and teeth are important for understanding human subsistence strategies and culture in the Pleistocene. However, it is difficult to associate these artefacts with specific individuals, unless they are found within burials. A non-destructive method has been developed to extract DNA from ancient bone and tooth artefacts, and analysis revealed that a female individual made the pendant.

NATURE (2023)

Article Genetics & Heredity

Historical Mitogenomic Diversity and Population Structuring of Southern Hemisphere Fin Whales

Danielle L. Buss, Lane M. Atmore, Maria H. Zicos, William P. Goodall-Copestake, Selina Brace, Frederick I. Archer, C. Scott Baker, Ian Barnes, Emma L. Carroll, Tom Hart, Andrew C. Kitchener, Richard Sabin, Angela L. Sremba, Caroline R. Weir, Jennifer A. Jackson

Summary: Fin whales have been extensively hunted, causing significant reductions in population size. Genetic samples from historical sources, such as bones and baleen, were used to assess the pre-whaling diversity of Southern Hemisphere fin whales. The results suggest that Southern Hemisphere fin whales are highly diverse and genetically distinct from Northern Hemisphere populations.
Article Archaeology

Tales from the Supplementary Information: Ancestry Change in Chalcolithic-Early Bronze Age Britain Was Gradual with Varied Kinship Organization

Thomas J. Booth, Joanna Bruck, Selina Brace, Ian Barnes

Summary: This article demonstrates how unnoticed details in the supplementary information of aDNA papers can offer crucial insights into patterns of ancestry change and genetic relatedness, particularly in the context of populations in Chalcolithic and Early Bronze Age Britain.

CAMBRIDGE ARCHAEOLOGICAL JOURNAL (2021)

暂无数据