Article
Multidisciplinary Sciences
Andre Elias Rodrigues Soares, Nikolaus Boroffka, Oskar Schroeder, Leonid Sverchkov, Norbert Benecke, Torsten Guenther
Summary: This study successfully identified a goitered gazelle specimen and confirmed hunting of the species in Central Asia during the Iron Age, using archaeogenomics. It represents the first ancient DNA and nuclear DNA sequences of this species. Due to limited genomic resources, a more in-depth analysis of the nuclear sequences was not possible.
ROYAL SOCIETY OPEN SCIENCE
(2022)
Article
Biochemical Research Methods
Eva Chocholova, Pavel Roudnicky, David Potesil, Dana Fialova, Karolina Krystofova, Eva Drozdova, Zbynek Zdrahal
Summary: This study proposes a protocol for the analysis of ancient proteins in dental calculus and a combined approach for subsequent extraction of ancient DNA. After testing and optimization, the protocol was successfully applied to ancient tooth samples, preserving the integrity and valuable information of the dental calculus.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Barry Shaw, Thomas Mcdonnell, Elizabeth Radley, Brian Thomas, Lynn Smith, Carol A. L. Davenport, Silvia Gonzalez, Anisur Rahman, Rob Layfield
Summary: Archaeological remains preserve proteins that can be used to study past events in human history. The functional proteins recovered from skeletal tissues can provide insights into the life-history of the remains. In this study, antibodies were purified from medieval human teeth and shown to retain their structure and demonstrate immunoreactivity against contemporary antigens. These ancient antibodies can reveal the long-term association between host immune factors and ancient microbes, providing a molecular memory of human health and immunity.
Article
Biochemistry & Molecular Biology
David G. Mahal
Summary: This study revealed the genetic affinities of Brahmins with foreign populations as well as with domestic non-Brahmin groups in India. By tracing Y-chromosome haplogroups and genetic markers, the deep ancient origins of Brahmins were identified, with their progenitors emerging from at least 12 different geographic regions worldwide. Additionally, the study found that 83% of Brahmins in the dataset belonged to four major haplogroups, two from Central Asia, one from the Fertile Crescent, and one of indigenous Indian origin.
MOLECULAR GENETICS AND GENOMICS
(2021)
Review
Green & Sustainable Science & Technology
Kornsorn Srikulnath, Nattakan Ariyaraphong, Worapong Singchat, Thitipong Panthum, Artem Lisachov, Syed Farhan Ahmad, Kyudong Han, Narongrit Muangmai, Prateep Duengkae
Summary: Mitochondrial displacement loop (mt D-loop) sequence analyses have improved assessments of genetic diversity and population dynamics of endangered species facing climate change and habitat loss. Tracking population haplotypes of these species using mitochondrial-based markers has advanced conservation genomics and biodiversity research. Studies on Asian elephants have used mt D-loop sequences to assess genetic diversity and population-scale hypotheses, shedding light on evolutionary processes and facilitating conservation efforts.
Article
Cell Biology
Xiaohong Deng, Dongmei Ji, Xinyuan Li, Yuping Xu, Yu Cao, Weiwei Zou, Chunmei Liang, Jordan Lee Marley, Zhiguo Zhang, Zhaolian Wei, Ping Zhou, Yajing Liu, Yunxia Cao
Summary: Certain mtDNA D-loop variants were found to be associated with decreased risk of PCOS in a Chinese population, but no significant correlation was found between D-loop polymorphisms and clinical characteristics within the PCOS group. Haplotype analysis suggested that a specific haplotype was significantly associated with decreased risk of PCOS.
Article
Biochemistry & Molecular Biology
Ricardo Rodriguez-Varela, Kristjan H. S. Moore, S. Sunna Ebenesersdottir, Gulsah Merve Kilinc, Anna Kjellstrom, Ludvig Papmehl-Dufay, Clara Alfsdotter, Birgitta Berglund, Loey Alrawi, Natalija Kashuba, Veronica Sobrado, Vendela Kempe Lagerholm, Edmund Gilbert, Gianpiero L. Cavalleri, Eivind Hovig, Ingrid Kockum, Tomas Olsson, Lars Alfredsson, Thomas F. Hansen, Thomas Werge, Arielle R. Munters, Carolina Bernhardsson, Birgitte Skar, Axel Christophersen, Gordon Turner-Walker, Shyam Gopalakrishnan, Eva Daskalaki, Ayca Omrak, Patxi Perez-Ramallo, Pontus Skoglund, Linus Girdland-Flink, Fredrik Gunnarsson, Charlotte Hedenstierna-Jonson, M. Thomas P. Gilbert, Kerstin Liden, Mattias Jakobsson, Lars Einarsson, Helena Victor, Maja Krzewinska, Torun Zachrisson, Jan Stora, Kari Stefansson, Agnar Helgason, Anders Gotherstrom
Summary: We analyze a 2,000-year genetic study of Scandinavia, using 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. Our findings reveal regional variation in gene flow from the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was common in Scandinavia during the Viking period, while eastern Baltic ancestry was more localized to Gotland and central Sweden. We also observe a decrease in current levels of external ancestry in some regions, suggesting less contribution from ancient immigrants to the modern Scandinavian gene pool compared to earlier periods.
Article
Multidisciplinary Sciences
Lane M. Atmore, Lourdes Martinez-Garcia, Daniel Makowiecki, Carl Andre, Lembi Lougas, James H. Barrett, Bastiaan Star
Summary: This study evaluates the past impacts of humans on the marine environment by studying the long-term population dynamics of Baltic herring. The research demonstrates the joint impact of climate change and human exploitation on marine species and highlights the role of historical ecology in conservation and management policies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Anthropology
Michal Marciak, Bartlomiej Szypula, Daniel Sobczynski
Summary: In recent years, there has been significant scientific interest in studying travel and mobility in the ancient Mediterranean and Near East. Although research on Late Antique Palestine has been extensive, the question of pre-Roman travel and mobility has received less attention. Recent archaeological discoveries in Jordan and Israel have challenged the previous belief that pre-Roman roads were not preserved, leading to new insights into the material remains of these ancient roads. This study aims to analyze the spatial and archaeological features of pre-Roman roads using different types of remote data as detection tools.
ARCHAEOLOGICAL AND ANTHROPOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Gunnar U. Neumann, Eirini Skourtanioti, Marta Burri, Elizabeth A. Nelson, Megan Michel, Alina N. Hiss, Photini J. P. McGeorge, Philip P. Betancourt, Maria A. Spyrou, Johannes Krause, Philipp W. Stockhammer
Summary: During the late 3rd millennium BCE, societal changes in the Eastern Mediterranean and Near East may have been influenced by infectious diseases, according to recent archaeogenetic research.
Article
Multidisciplinary Sciences
Linda M. Seymour, Janille Maragh, Paolo Sabatini, Michel Di Tommaso, James C. Weaver, Admir Masic
Summary: This study investigates the durability of ancient Roman concretes using a multiscale correlative elemental and chemical mapping approach. The analysis reveals that the Romans employed hot mixing with quicklime in conjunction with or instead of slaked lime, resulting in the retention of large surface area lime clasts within the mortar matrix. Inspired by these findings, modern lime clast-containing cementitious mixtures were developed and tested, demonstrating their self-healing potential and paving the way for more durable and sustainable concrete formulations.
Article
Endocrinology & Metabolism
Yang Chen, Wei-jia Wu, Li-wei Xing, Xiao-juan Zhang, Jing Wang, Xiao-yan Xia, Rui Zhao, Rong Zhao
Summary: This study examined the correlations between mtDNA D-loop, its haplotypes, and PCOS in the Chinese population, and found that certain mtDNA D-loop mutations and haplotypes may confer protection against PCOS in Chinese women. In addition, elevated mtDNA copy number may serve as an indicator during early stages of PCOS.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Eadaoin Harney, Olivia Cheronet, Daniel M. Fernandes, Kendrs Sirak, Matthew Mah, Rebecca Bernardos, Nicole Adamski, Nasreen Broomandkhoshbacht, Kimberly Callan, Ann Marie Lawson, Jonas Oppenheimer, Kristin Stewardson, Fatma Zalzala, Alexandra Anderes, Francesca Candilio, Mihai Constantinescu, Alfredo Coppa, Ion Ciobanu, Janos Dani, Zsolt Gallina, Francesco Genchi, Emese Gyongyver Nagy, Tamas Hajdu, Magdolna Hellebrandt, Antonia Horvath, Agnes Kiraly, Krisztian Kiss, Barbara Kolozsi, Peter Kovacs, Kitti Koehler, Michaela Lucci, Ildiko Pap, Sergiu Popovici, Pal Raczky, Angela Simalcsik, Tamas Szeniczey, Sergey Vasilyev, Cristian Virag, Nadin Rohland, David Reich, Ron Pinhasi
Summary: Destructive sampling methods for ancient DNA, such as drilling or cutting bones and teeth, can lead to concerns and loss, but a minimally destructive method focusing on tooth roots' cementum offers a safe and efficient alternative. The minimally destructive method provides ancient DNA of comparable quality to destructive sampling, with rigorous cleaning procedures reducing external contaminants typically removed through physical methods.
Article
Biochemistry & Molecular Biology
Lidia Kozak, Andrzej Michalowski, Jedrzej Proch, Michal Krueger, Octavian Munteanu, Przemyslaw Niedzielski
Summary: This study presents the determination of iron forms in archaeological pottery using a simple test and various spectroscopy techniques. The results have been applied to archaeometric studies for recognizing pottery production technology, surpassing traditional color analysis.
Article
Computer Science, Artificial Intelligence
Hafeez Anwar, Saeed Anwar, Sebastian Zambanini, Fatih Porikli
Summary: The study classifies ancient Roman Republican coins by recognizing their reverse motifs. A novel network model, CoinNet, is proposed, along with a large and diverse image dataset of the coins. The model achieves high classification accuracy and outperforms conventional methods.
PATTERN RECOGNITION
(2021)
Article
Biochemistry & Molecular Biology
Ricardo Rodriguez-Varela, Kristjan H. S. Moore, S. Sunna Ebenesersdottir, Gulsah Merve Kilinc, Anna Kjellstrom, Ludvig Papmehl-Dufay, Clara Alfsdotter, Birgitta Berglund, Loey Alrawi, Natalija Kashuba, Veronica Sobrado, Vendela Kempe Lagerholm, Edmund Gilbert, Gianpiero L. Cavalleri, Eivind Hovig, Ingrid Kockum, Tomas Olsson, Lars Alfredsson, Thomas F. Hansen, Thomas Werge, Arielle R. Munters, Carolina Bernhardsson, Birgitte Skar, Axel Christophersen, Gordon Turner-Walker, Shyam Gopalakrishnan, Eva Daskalaki, Ayca Omrak, Patxi Perez-Ramallo, Pontus Skoglund, Linus Girdland-Flink, Fredrik Gunnarsson, Charlotte Hedenstierna-Jonson, M. Thomas P. Gilbert, Kerstin Liden, Mattias Jakobsson, Lars Einarsson, Helena Victor, Maja Krzewinska, Torun Zachrisson, Jan Stora, Kari Stefansson, Agnar Helgason, Anders Gotherstrom
Summary: We analyze a 2,000-year genetic study of Scandinavia, using 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. Our findings reveal regional variation in gene flow from the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was common in Scandinavia during the Viking period, while eastern Baltic ancestry was more localized to Gotland and central Sweden. We also observe a decrease in current levels of external ancestry in some regions, suggesting less contribution from ancient immigrants to the modern Scandinavian gene pool compared to earlier periods.
Article
Biochemistry & Molecular Biology
Charles Christian Riis Hansen, Aki Jarl Laruson, Jacob Agerbo Rasmussen, Jesus Adrian Chimal Ballesteros, Mikkel-Holger S. Sinding, Gunnar T. T. Hallgrimsson, Menja von Schmalensee, Robert A. A. Stefansson, Kristinn Haukur Skarphedinsson, Aili Lage Labansen, Madis Leivits, Christian Sonne, Rune Dietz, Kim Skelmose, David Boertmann, Igor Eulaers, Michael D. D. Martin, Agnar S. S. Helgason, M. Thomas P. Gilbert, Snaebjorn Palsson
Summary: Divergence in white-tailed eagle populations across Europe and the North-East Atlantic is observed, with the greatest differentiation between island and mainland populations. The island populations have a common ancestry from a mainland population and show signs of inbreeding and little genetic variation. Temporal differences also indicate persistent regional populations despite potential admixture. These patterns may have been shaped by historical events such as glaciation, colonization, human expansion, and persecution.
Article
Multidisciplinary Sciences
Ryan R. Germain, Shaohong Feng, Lucas Buffan, Carlos P. Carmona, Guangii Chen, Gary R. Graves, Joseph A. Tobias, Carsten Rahbek, Fumin Lei, Jon Fjeldsa, Peter A. Hosner, M. Thomas P. Gilbert, Guojie Zhang, David Nogues-Bravo
Summary: By combining morphological, ecological, and life-history trait data with genomic-based estimates of changing effective population size, this study explores the demographic-based shifts in avian functional diversity over the past million years and under pre-anthropogenic climate warming. The results show that functional diversity remained relatively stable over this period, but significant changes occurred in some key areas of trait space due to changing species abundances. Furthermore, the study identifies the vulnerability of different regions of functional space among taxa, enhancing our understanding of losses of biosphere integrity before human disturbances and contemporary biodiversity loss.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biotechnology & Applied Microbiology
Soren B. Hansen, Davide Bozzi, Sarah S. T. Mak, Cecilie G. Clausen, Tue K. Nielsen, Miyako Kodama, Lars H. Hansen, M. Thomas P. Gilbert, Morten T. Limborg
Summary: Obtaining desired phenotypic traits in aquacultural production of Atlantic salmon is still a challenge, and the presence of host-associated microorganisms might contribute to this challenge. Understanding the factors that shape the microbiota is crucial for manipulating it towards desired host traits. In this study, DNA methylation differences associated with a tenacibaculosis outbreak and microbiota displacement in Atlantic salmon were investigated, revealing potential genes involved in host-microbiota interactions and the importance of considering epigenetic factors in manipulating farmed fish microbiota.
Article
Ecology
Jacob A. Rasmussen, Pia Kiilerich, Abdullah S. Madhun, Rune Waagbo, Erik-Jan R. Lock, Lise Madsen, M. Thomas P. Gilbert, Karsten Kristiansen, Morten T. Limborg
Summary: Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform our understanding of adaptive phenotypic traits. This study reveals a strong co-evolution between the population structure of Atlantic salmon and nucleotide variability of the intestinal Mycoplasma populations, indicating an interplay between the host and its resident bacteria.
Article
Multidisciplinary Sciences
Lucie A. Bergeron, Soren Besenbacher, Jiao Zheng, Panyi Li, Mads Frost Bertelsen, Benoit Quintard, Joseph I. Hoffman, Zhipeng Li, Judy St Leger, Changwei Shao, Josefin Stiller, M. Thomas P. Gilbert, Mikkel H. Schierup, Guojie Zhang
Summary: We sequenced and compared high-coverage genomes of 151 parent-offspring trios from 68 species of vertebrates and found that the per-generation mutation rate varies greatly among species, with males having higher rates than females in mammals and birds. We identified generation time, age at maturity, and species-level fecundity as key factors influencing this variation. Species with larger long-term effective population sizes tend to have lower mutation rates, supporting the drift barrier hypothesis. Domesticated animals with shorter generation times display exceptionally high yearly mutation rates, emphasizing the importance of generation time in mutation rate evolution.
Article
Multidisciplinary Sciences
Pnina Cohen, Roberto Bacilieri, Jazmin Ramos-Madrigal, Eyal Privman, Elisabetta Boaretto, Audrey Weber, Daniel Fuks, Ehud Weiss, Tali Erickson-Gini, Scott Bucking, Yotam Tepper, Deborah Cvikel, Joshua Schmidt, M. Thomas P. Gilbert, Nathan Wales, Guy Bar-Oz, Meirav Meiri
Summary: Recent excavations in the Negev Highlands of southern Israel revealed a society that established large-scale viticulture in an arid environment. By analyzing grapevine pips using genome-wide sequencing and radiocarbon dating, researchers found evidence of continuous grape cultivation in the Southern Levant for centuries. The genetically diverse pips also provided insights into ancient cultivation strategies and their contribution to agricultural productivity and food security.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Ostaizka Aizpurua, Kees Blijleven, Urvish Trivedi, M. Thomas P. Gilbert, Antton Alberdi
Summary: The impact of microorganisms on the evolution of animal hosts is a significant question in biology, yet the underlying mechanisms and causal relationships remain unresolved. Gut-on-a-chip models offer a novel approach to studying how animals perceive and respond to microbes, providing insights into the role of host-microbiota interactions in animal evolution.
TRENDS IN MICROBIOLOGY
(2023)
Article
Cell Biology
Pei Zhang, Yuanzhen Zhu, Qunfei Guo, Ji Li, Xiaoyu Zhan, Hao Yu, Nianxia Xie, Huishuang Tan, Nina Lundholm, Lydia Garcia-Cuetos, Michael D. Martin, Meritxell Anto Subirats, Yi-Hsien Su, Inaki Ruiz-Trillo, Mark Q. Martindale, Jr-Kai Yu, M. Thomas P. Gilbert, Guojie Zhang, Qiye Li
Summary: By analyzing the RNA editomes of 22 Holozoa species, we provide substantial evidence that A-to-I mRNA editing is a regulatory innovation that originated in the last common ancestor of extant metazoans. This ancient biochemical process is preserved in most metazoans and primarily targets endogenous dsRNA formed by young repeats. We also find that intermolecular pairing of sense-antisense transcripts is an important mechanism for forming dsRNA substrates for A-to-I editing in some lineages. Recoding editing is rarely shared across lineages but preferentially targets genes involved in neural and cytoskeleton systems in bilaterians. We conclude that metazoan A-to-I editing initially emerged as a safeguard mechanism against repeat-derived dsRNA and was later co-opted into diverse biological processes due to its mutagenic nature.
Article
Ecology
Ryan R. Germain, Shaohong Feng, Guangji Chen, Gary R. Graves, Joseph A. Tobias, Carsten Rahbek, Fumin Lei, Jon Fjeldsa, Peter A. Hosner, M. Thomas P. Gilbert, Guojie Zhang, David Nogues-Bravo
Summary: Using whole-genome sequence data, this study reconstructs the demographic histories of 263 bird species over the past million years and identifies networks of interacting morphological and life history traits associated with changes in effective population size (Ne) in response to climate warming and cooling. The results highlight the direct and indirect effects of key traits representing dispersal, reproduction, and survival on long-term demographic responses to climate change, thus identifying the traits most likely to influence population responses to ongoing climate warming.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Linett Rasmussen, Claudia Fontsere, Ivan D. Soto-Calderon, Rosamira Guillen, Anne Savage, Anders Johannes Hansen, Christina Hvilsom, M. Thomas P. Gilbert
Summary: The critically endangered cotton-top tamarin has been threatened by human activities, causing habitat loss and population decline. This study aimed to establish a genetic baseline through temporal sampling to understand the genetic makeup before anthropogenic impacts. By resequencing genomes from historical and modern samples, two populations were identified, separated historically by mountain ranges. The modern populations show signs of inbreeding and loss of genomic diversity, likely due to population reduction and ongoing habitat loss. However, there is no evidence of an increase in genetic load. The historical genetic baseline can provide insight into the alteration of current populations and inform conservation decision-making.
Article
Ecology
German Hernandez-Alonso, Jazmin Ramos-Madrigal, Xin Sun, Camilla Hjorth Scharff-Olsen, Mikkel-Holger S. Sinding, Nuno F. F. Martins, Marta Maria Ciucani, Sarah S. T. Mak, Liam Thomas Lanigan, Cecilie G. G. Clausen, Jong Bhak, Sungwon Jeon, Changjae Kim, Kyung Yeon Eo, Seong-Ho Cho, Bazartseren Boldgiv, Gankhuyag Gantulga, Zunduibaatar Unudbayasgalan, Pavel A. A. Kosintsev, Hans K. K. Stenoien, M. Thomas P. Gilbert, Shyam Gopalakrishnan
Summary: By sequencing and analyzing the genomes of a Korean wolf from the early 20th century and a captive wolf from the Pyongyang Central Zoo, it was found that the Korean wolf shares genetic ancestry with other East Asian wolf populations, indicating it is not a distinct taxonomic lineage. Additionally, regional patterns of wolf population structure and admixture in East Asia were identified, highlighting the importance of conservation efforts in the Korean Peninsula and on a regional scale. The study also revealed that the captive wolf is genetically more similar to wolves from the Tibetan Plateau, suggesting that its inclusion in Korean wolf conservation programs might not be beneficial.
ECOLOGY AND EVOLUTION
(2023)
Article
Biology
Edward Rice, Antton Alberdi, James Alfieri, Giridhar Athrey, Jennifer Balacco, Philippe Bardou, Heath Blackmon, Mathieu Charles, Hans Cheng, Olivier Fedrigo, Steven Fiddaman, Giulio Formenti, Laurent Frantz, M. Thomas Gilbert, Cari Hearn, Erich Jarvis, Christophe Klopp, Sofia Marcos, Andrew Mason, Deborah Velez-Irizarry, Luohao Xu, Wesley Warren
Summary: This research presents a pangenome model for domestic chickens consisting of thirty assemblies from different breeds and research lines. It demonstrates how this model can be used to catalogue structural variants in modern breeds and unravel complex nested variations. The study shows that aligning short reads from diverse wild and domestic chickens to this pangenome reduces reference bias and allows for accurate genotyping of complex structural variants.
Article
Biochemistry & Molecular Biology
German Hernandez-Alonso, Jazmin Ramos-Madrigal, Hein van Grouw, Marta Maria Ciucani, Emily Louisa Cavill, Mikkel-Holger S. Sinding, Shyam Gopalakrishnan, George Pacheco, M. Thomas P. Gilbert
Summary: This study used whole-genome sequencing data to investigate the population structure, domestication history, and taxonomy of the rock dove Columba livia. The results revealed the basal position of the West African subspecies, gene-flow between the rock dove's sister species, and proposed a model for the rock dove's evolution based on the refugia theory. Additionally, the study identified at least one domestication event in the Levant that gave rise to all analyzed domestic breeds.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Fisheries
Mikkel Skovrind, George Pacheco, Emil Aputsiaq Flindt Christensen, Shyam Gopalakrishnan, Katharina Fietz, Tore Hejl Holm-Hansen, Filipe Garrett Vieira, Marcus Anders Krag, Henrik Carl, M. Thomas P. Gilbert, Morten Tange Olsen, Peter Rask Moller
Summary: Environmental variation can lead to local adaptations in wild species. In the case of European perch, a specialised brackish water variant has developed in the Baltic Sea region. However, little is known about the mechanisms underlying the perch’s adaptation to the Baltic Sea. Through genetic analysis, it was found that brackish water perch show distinct genetic differences compared to freshwater perch, with higher levels of gene flow. Selection analysis suggests that genomic adaptation played a role in the perch’s colonization of the Baltic Sea.
FISHERIES RESEARCH
(2023)
