Editorial Material
Multidisciplinary Sciences
Annemieke Milks
Summary: Understanding the timeline of technological developments is important in studying early societies. The discovery of a structure made from shaped wood in Africa provides valuable clues about our hominin relatives.
News Item
Multidisciplinary Sciences
Ewen Callaway
Summary: The majority of sequences are from individuals in Western Eurasia, however, there is an increasing number of samples from other regions.
Article
Multidisciplinary Sciences
Axel Timmermann, Kyung-Sook Yun, Pasquale Raia, Jiaoyang Ruan, Alessandro Mondanaro, Elke Zeller, Christoph Zollikofer, Marcia Ponce de Leon, Danielle Lemmon, Matteo Willeit, Andrey Ganopolski
Summary: The study demonstrates that climate changes over the past 2 million years have had a significant impact on the distribution of hominin species. Early hominins settled in environments with weak climate variability, while after the mid-Pleistocene transition, humans became global wanderers adapting to a wide range of climatic gradients. Phased climate disruptions in southern Africa and Eurasia further contributed to the evolutionary transformation of Homo heidelbergensis populations into Homo sapiens and Neanderthals.
Article
Multidisciplinary Sciences
Marsha C. Wibowo, Zhen Yang, Maxime Borry, Alexander Huebner, Kun D. Huang, Braden T. Tierney, Samuel Zimmerman, Francisco Barajas-Olmos, Cecilia Contreras-Cubas, Humberto Garcia-Ortiz, Angelica Martinez-Hernandez, Jacob M. Luber, Philipp Kirstahler, Tre Blohm, Francis E. Smiley, Richard Arnold, Sonia A. Ballal, Sunje Johanna Pamp, Julia Russ, Frank Maixner, Omar Rota-Stabelli, Nicola Segata, Karl Reinhard, Lorena Orozco, Christina Warinner, Meradeth Snow, Steven LeBlanc, Aleksandar D. Kostic
Summary: This study used ancient fecal samples to study microbial genomes, revealing that these samples are more similar to non-industrialized human gut microbiomes and contain previously unknown microbial species. The fecal samples showed lower abundance of antibiotic resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes.
Editorial Material
Multidisciplinary Sciences
Dyani Lewis
Summary: Fieldwork is currently being conducted in central China to excavate a rare and well-preserved specimen.
Article
Geography, Physical
G. Ferentinos, M. Gkioni, M. Prevenios, M. Geraga, G. Papatheodorou
Summary: This paper challenges previous understandings of Aegean Sea palaeo-geography by showing that the Central Aegean Island Chain was insular from surrounding landmasses, providing evidence that archaic hominins sea-crossed the Aegean Sea as early as 450 ka BP. The study also suggests that they were encouraged by favorable land/seascape configuration and spread to the Circum-Mediterranean basin via two converging routes.
QUATERNARY INTERNATIONAL
(2023)
News Item
Multidisciplinary Sciences
Colin Barras
Summary: Archaeological evidence suggests that humans developed numbers tens of thousands of years ago, and scholars are now exploring the first detailed hypotheses about this transformative invention.
Article
Ecology
Colin M. Brand, Laura L. Colbran, John A. Capra
Summary: Alternative splicing plays a crucial role in adaptation and divergence. By utilizing the SpliceAI algorithm, researchers have identified thousands of splice-altering variants in archaic hominins. These archaic-specific variants are more commonly found in the genomes of Neanderthals and Denisovans and may contribute to phenotypic differences among hominins.
NATURE ECOLOGY & EVOLUTION
(2023)
Editorial Material
Multidisciplinary Sciences
Louise Humphrey, Abdeljalil Bouzouggar
Summary: Genomic data from bones and teeth found at archaeological sites across Morocco reveal a more intricate spread of Neolithic farmers and pastoralists into northwest Africa than previously believed.
Editorial Material
Biochemistry & Molecular Biology
Yichen Liu, E. Andrew Bennett, Qiaomei Fu
Summary: Ancient DNA techniques have advanced significantly in the past decade, enabling large-scale research independent of human remains. Future directions include expanding research scope and gaining insights into present-day human health.
Article
Archaeology
Pierre Zalloua, Nada Elias, Anna Senovska, Catherine Collins, Anna Gosling, Samar Karam, Amine-Jules Iskandar, Elizabeth Matisoo-Smith
Summary: Historic records reveal the exhumation and transfer of 17 Maronite patriarchs' remains from their original burial site to a secondary collective burial. Using various methods, including DNA analysis, the researchers sought to confirm the identity of the patriarchs' remains, particularly that of patriarch Estephan El Douaihy. Through the examination of records, osteological analysis, and genetic testing, it was concluded that the 16 complete skulls discovered in the burial likely belong to the patriarchs exhumed in 1909.
JOURNAL OF CULTURAL HERITAGE
(2023)
Editorial Material
Multidisciplinary Sciences
Muge Durusu-Tanriover
Summary: An assessment of juniper tree-ring samples from central Turkey, together with other types of dating analysis, demonstrate that a devastating drought in 1198-1196 BC contributed to the end of the Hittite empire.
Article
Biodiversity Conservation
John K. Millhauser, Timothy K. Earle
Summary: This article reviews the impact of human activities on biodiversity through archaeological and ethnographic cases, which cover different ecologies, population densities, and economies. The author points out that while humans have always transformed ecosystems, many pre-industrial societies maintained diverse and stable environments. Present-day solutions should involve local communities, especially Indigenous and traditional societies, empowering them to shape policies and achieve conservation goals.
BIOLOGICAL CONSERVATION
(2022)
News Item
Multidisciplinary Sciences
Ewen Callaway
Summary: High-profile researchers claim that Homo naledi, despite having small brains, displayed advanced behaviors like burials, but peer reviewers argue that there is lack of evidence.
Article
Multidisciplinary Sciences
Muriel Gros-Balthazard, Jonathan M. Flowers, Khaled M. Hazzouri, Sylvie Ferrand, Frederique Aberlenc, Sarah Sallon, Michael D. Purugganan
Summary: Researchers recovered seven date palm seeds from archaeological sites in the Southern Levant, dating from the fourth century BCE to the second century CE, which were germinated to yield viable plants. Whole-genome sequencing of these ancient samples showed genetic relationships between the ancient Judean date palms and modern West Asian and North African date palm varieties. These findings provide insights into crop evolution and the introgression of genetic features from the Cretan palm Phoenix theophrasti into modern North African date palm populations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Xuexue Liu, Yanli Zhang, Wujun Liu, Yefang Li, Jianfei Pan, Yabin Pu, Jianlin Han, Ludovic Orlando, Yuehui Ma, Lin Jiang
Summary: This study identified the causal regulatory mutation underlying small body size in Chinese ponies and revealed size as one of the main selection targets of past Chinese breeders.
Article
Biochemistry & Molecular Biology
Tomasz Suchan, Mariya A. Kusliy, Naveed Khan, Lorelei Chauvey, Laure Tonasso-Calviere, Stephanie Schiavinato, John Southon, Marcel Keller, Keiko Kitagawa, Johannes Krause, Alexander N. Bessudnov, Alexander A. Bessudnov, Alexander S. Graphodatsky, Silvia Valenzuela-Lamas, Jaroslaw Wilczynski, Sylwia Pospula, Krzysztof Tunia, Marek Nowak, Magdalena Moskal-delHoyo, Alexey A. Tishkin, Alexander J. E. Pryor, Alan K. Outram, Ludovic Orlando
Summary: DNA hybridization-capture techniques allow researchers to target specific genomic regions for sequencing, which is especially helpful for analyzing ancient DNA. HyRAD, a cost-effective alternative to commercial capture protocols, demonstrated its performance in obtaining authentic aDNA data from osseous remains, even in samples with low endogenous content. This approach utilizes double enzymatic restriction of DNA extracts to produce RNA probes that cover only a fraction of the genome, serving as baits for capturing homologous fragments from aDNA libraries.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Tomasz Suchan, Lorelei Chauvey, Marine Poullet, Laure Tonasso-Calviere, Stephanie Schiavinato, Pierre Clavel, Benoit Clavel, Sebastien Lepetz, Andaine Seguin-Orlando, Ludovic Orlando
Summary: Preservation of ancient DNA in subfossil specimens allows retrieval of genetic information from the past. Capture techniques are used to economically retrieve sequence data, while USER treatment reduces sequence errors. This study shows that USER treatment can negatively impact capture efficacy and introduce experimental bias.
MOLECULAR ECOLOGY RESOURCES
(2022)
Correction
Multidisciplinary Sciences
Yucheng Wang, Mikkel Winther Pedersen, Inger Greve Alsos, Bianca De Sanctis, Fernando Racimo, Ana Prohaska, Eric Coissac, Hannah Lois Owens, Marie Kristine Foreid Merkel, Antonio Fernandez-Guerra, Alexandra Rouillard, Youri Lammers, Adriana Alberti, France Denoeud, Daniel Money, Anthony H. Ruter, Hugh McColl, Nicolaj Krog Larsen, Anna A. Cherezova, Mary E. Edwards, Grigory B. Fedorov, James Haile, Ludovic Orlando, Lasse Vinner, Thorfinn Sand Korneliussen, David W. Beilman, Anders A. Bjork, Jialu Cao, Christoph Dockter, Julie Esdale, Galina Gusarova, Kristian K. Kjeldsen, Jan Mangerud, Jeffrey T. Rasic, Birgitte Skadhauge, John Inge Svendsen, Alexei Tikhonov, Patrick Wincker, Yingchun Xing, Yubin Zhang, Duane G. Froese, Carsten Rahbek, David Nogues Bravo, Philip B. Holden, Neil R. Edwards, Richard Durbin, David J. Meltzer, Kurt H. Kjaer, Per Moller, Eske Willerslev
Article
Biology
Dawei Cai, Siqi Zhu, Mian Gong, Naifan Zhang, Jia Wen, Qiyao Liang, Weilu Sun, Xinyue Shao, Yaqi Guo, Yudong Cai, Zhuqing Zheng, Wei Zhang, Songmei Hu, Xiaoyang Wang, He Tian, Youqian Li, Wei Liu, Miaomiao Yang, Jian Yang, Duo Wu, Ludovic Orlando, Yu Jiang
Summary: The rich fossil record of the equid family has provided valuable insights into the macroevolutionary changes in this group. This study analyzed archaeological specimens from Northern China and sequenced the complete genome of Equus ovodovi, a species belonging to the Sussemionus subgenus. The results revealed that this lineage survived until approximately 3500 years ago, despite population collapse during the Last Glacial Maximum and human expansion in East Asia. The study also highlighted the importance of genetic diversity for species' survival.
Article
Biochemical Research Methods
Xuexue Liu, Ludovic Orlando
Summary: mapDATAge is a software designed to help non-computer professionals visualize ancient DNA datasets by mapping allele, haplogroup, and/or ancestry distributions through space and time. It enables collaborative data sharing and facilitates the assessment of spatiotemporal patterns of genetic changes.
Article
Multidisciplinary Sciences
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.
Review
Genetics & Heredity
Evelyn Jane Collen, Angad Singh Johar, Joao C. Teixeira, Bastien Llamas
Summary: This study examines the impacts of imported infectious diseases on the immune system of Indigenous peoples in America during early European contact. The findings suggest that post-contact Indigenous immune adaptation is complex and influenced by various factors, including selection exerted by introduced pathogens.
FRONTIERS IN GENETICS
(2022)
Article
Microbiology
Gina L. Guzzo, Murthy N. Mittinty, Bastien Llamas, Jane M. Andrews, Laura S. Weyrich
Summary: It is known that the bacterial gut microbiome is altered in inflammatory bowel disease (IBD), but the role of eukaryotic microorganisms in IBD is less understood. This study characterized the eukaryotic microbial communities in IBD patients and found higher prevalence of fungi and lower prevalence of protozoa compared to healthy individuals. Disease state, age, and BMI were associated with the prevalence and abundance of these eukaryotes. The study also found that the eukaryotic gut microbiome varied over time in IBD patients who received fecal transplants. The findings suggest that future studies should consider including eukaryotic microbes when characterizing the gut microbiome in IBD.
Review
Genetics & Heredity
Leonard Taufik, Joao C. Teixeira, Bastien Llamas, Herawati Sudoyo, Raymond Tobler, Gludhug A. Purnomo
Summary: Genomic sequence data provides novel insights into human ancestry and migratory history. However, many Indigenous populations have been excluded from genomic surveys, hindering a comprehensive understanding of these fundamental questions. This review summarizes key findings from population genetic and phylogeographic studies in Wallacea and Sahul, highlighting their importance in addressing human evolutionary questions.
Article
Biochemistry & Molecular Biology
Stefanie Wagner, Andaine Seguin-Orlando, Jean-Charles Leple, Thibault Leroy, Celine Lalanne, Karine Labadie, Jean-Marc Aury, Sandy Poirier, Patrick Wincker, Christophe Plomion, Antoine Kremer, Ludovic Orlando
Summary: Whole genome characterizations based on ancient DNA have provided valuable insights into the evolutionary origins and adaptive processes of modern cultivars. However, there has been a lack of ancient genome sequences for trees, in contrast to the availability of multiple ancient reference genomes for important crops. This study generated the first ancient tree genomes, revealing the species composition and timing of leaf unfolding for ancient trees, and expanding the applications of ancient wood in enhancing our understanding of forest ecosystem responses to past changes.
Editorial Material
Multidisciplinary Sciences
Ludovic Orlando
Summary: An extensive genomic time series has been conducted on 356 humans from ice-age Europe, showing the impact of climate change on the migration patterns and cultural development of hunter-gatherer populations.
Editorial Material
Multidisciplinary Sciences
Rasmus Gronfeldt Winther, Eske Willerslev
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Dawn A. Lewis, Rebecca Simpson, Azure Hermes, Alex Brown, Bastien Llamas
Summary: The rise of sedimentary ancient DNA studies has provided new possibilities for studying past environments by using sediments to identify organisms. However, managing this substrate in Indigenous Australian contexts requires special considerations due to the cultural significance of the genetic information obtained. Benefit sharing, particularly the integration of Traditional Knowledges, is crucial in ensuring research outcomes are shared equitably with Indigenous communities and that the research is conducted ethically.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Cell Biology
Neerjah Skantharajah, Shakuntala Baichoo, Tiffany F. Boughtwood, Esmeralda Casas-Silva, Subhashini Chandrasekharan, Sanjay M. Dave, Khalid A. Fakhro, Aida B. Falcon de Vargas, Sylvia S. Gayle, Vivek K. Gupta, Rachele Hendricks-Sturrup, Ashley E. Hobb, Stephanie Li, Bastien Llamas, Catalina Lopez-Correa, Mavis Machirori, Jorge Melendez-Zajgla, Mareike A. Millner, Angela J. H. Page, Laura D. Pagilone, Maili C. Raven-Adams, Lindsa Smith, Ericka M. Thomas, Judi Kumthini, Manuel Corpas
Summary: The lack of diversity hinders equitable leadership and access to precision medicine in the field of genomics for health. To address this issue, the Global Alliance for Genomics and Health has implemented measures to promote diversity and inclusion in its standards and membership.
