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JOURNAL ARTICLE
Şevval Aktürk, Igor Mapelli, Merve N Güler, Kanat Gürün, Büşra Katırcıoğlu, Kıvılcım Başak Vural, Ekin Sağlıcan, Mehmet Çetin, Reyhan Yaka, Elif Sürer, Gözde Atağ, Sevim Seda Çokoğlu, Arda Sevkar, N Ezgi Altınışık, Dilek Koptekin, Mehmet Somel
There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs...
April 27, 2024: Molecular Ecology Resources
#2
JOURNAL ARTICLE
Praveen Halagali, Aparna Inamdar, Jagroop Singh, Amit Anand, Poulami Sadhu, Rashmi Pathak, Himanshu Sharma, Deepak Biswas
Comprehensive and effective care techniques have become essential due to the global epidemic dimensions of metabolic disorders, including diabetes, obesity, and cardiovascular ailments. Recent research highlights the potential of dietary supplements, herbal extracts, and phytochemicals in treating metabolic diseases. This abstract conveys the current state of the science in this field by highlighting these findings' underlying mechanisms and potential therapeutic applications. Plant-based diets contain naturally occurring bioactive molecules termed phytochemicals, which have shown promise in treating various metabolic illnesses...
April 26, 2024: Endocrine, Metabolic & Immune Disorders Drug Targets
#3
JOURNAL ARTICLE
Stephanie Andaluz, Bojin Zhao, Siddharth Sinha, Philip Naderev Panuringan Lagniton, Diogo Alpuim Costa, Xiaofan Ding, Miguel Brito, San Ming Wang
BACKGROUND: Admixture occurs between different ethnic human populations. The global colonization in recent centuries by Europeans led to the most significant admixture in human history. While admixture may enhance genetic diversity for better fitness, it may also impact on human health by transmitting genetic variants for disease susceptibility in the admixture population. The admixture by Portuguese global exploration initiated in the 15th century has reached over 20 million of Portuguese-heritage population worldwide...
April 27, 2024: BMC Genomics
#4
REVIEW
Alberto J Taurozzi, Patrick L Rüther, Ioannis Patramanis, Claire Koenig, Ryan Sinclair Paterson, Palesa P Madupe, Florian Simon Harking, Frido Welker, Meaghan Mackie, Jazmín Ramos-Madrigal, Jesper V Olsen, Enrico Cappellini
In temperate and subtropical regions, ancient proteins are reported to survive up to about 2 million years, far beyond the known limits of ancient DNA preservation in the same areas. Accordingly, their amino acid sequences currently represent the only source of genetic information available to pursue phylogenetic inference involving species that went extinct too long ago to be amenable for ancient DNA analysis. Here we present a complete workflow, including sample preparation, mass spectrometric data acquisition and computational analysis, to recover and interpret million-year-old dental enamel protein sequences...
April 26, 2024: Nature Protocols
#5
JOURNAL ARTICLE
Alexandros Heraclides, Aris Aristodemou, Andrea N Georgiou, Marios Antoniou, Elisabeth Ilgner, Leonidas-Romanos Davranoglou
Archaeological evidence supports sporadic seafaring visits to the Eastern Mediterranean island of Cyprus by Epipaleolithic hunter-gatherers over 12,000 years ago, followed by permanent settlements during the early Neolithic. The geographical origins of these early seafarers have so far remained elusive. By systematically analysing all available genomes from the late Pleistocene to early Holocene Near East (c. 14,000-7000 cal BCE), we provide a comprehensive overview of the genetic landscape of the early Neolithic Fertile Crescent and Anatolia and infer the likely origins of three recently published genomes from Kissonerga-Mylouthkia (Cypriot Late Pre-Pottery Neolithic B, c...
April 26, 2024: Scientific Reports
#6
JOURNAL ARTICLE
David L Lentz, Trinity L Hamilton, Stephanie A Meyers, Nicholas P Dunning, Kathryn Reese-Taylor, Armando Anaya Hernández, Debra S Walker, Eric J Tepe, Atasta Flores Esquivel, Alison A Weiss
For millennia, healing and psychoactive plants have been part of the medicinal and ceremonial fabric of elaborate rituals and everyday religious practices throughout Mesoamerica. Despite the essential nature of these ritual practices to the societal framework of past cultures, a clear understanding of the ceremonial life of the ancient Maya remains stubbornly elusive. Here we record the discovery of a special ritual deposit, likely wrapped in a bundle, located beneath the end field of a Late Preclassic ballcourt in the Helena complex of the Maya city of Yaxnohcah...
2024: PloS One
#7
Iosif Lazaridis, Nick Patterson, David Anthony, Leonid Vyazov, Romain Fournier, Harald Ringbauer, Iñigo Olalde, Alexander A Khokhlov, Egor P Kitov, Natalia I Shishlina, Sorin C Ailincăi, Danila S Agapov, Sergey A Agapov, Elena Batieva, Baitanayev Bauyrzhan, Zsolt Bereczki, Alexandra Buzhilova, Piya Changmai, Andrey A Chizhevsky, Ion Ciobanu, Mihai Constantinescu, Marietta Csányi, János Dani, Peter K Dashkovskiy, Sándor Évinger, Anatoly Faifert, Pavel N Flegontov, Alin Frînculeasa, Mădălina N Frînculeasa, Tamás Hajdu, Tom Higham, Paweł Jarosz, Pavol Jelínek, Valeri I Khartanovich, Eduard N Kirginekov, Viktória Kiss, Alexandera Kitova, Alexeiy V Kiyashko, Jovan Koledin, Arkady Korolev, Pavel Kosintsev, Gabriella Kulcsár, Pavel Kuznetsov, Rabadan Magomedov, Mamedov Aslan Malikovich, Eszter Melis, Vyacheslav Moiseyev, Erika Molnár, Janet Monge, Octav Negrea, Nadezhda A Nikolaeva, Mario Novak, Maria Ochir-Goryaeva, György Pálfi, Sergiu Popovici, Marina P Rykun, Tatyana M Savenkova, Vladimir P Semibratov, Nikolai N Seregin, Alena Šefčáková, Mussayeva Raikhan Serikovna, Irina Shingiray, Vladimir N Shirokov, Angela Simalcsik, Kendra Sirak, Konstantin N Solodovnikov, Judit Tárnoki, Alexey A Tishkin, Viktov Trifonov, Sergey Vasilyev, Ali Akbari, Esther S Brielle, Kim Callan, Francesca Candilio, Olivia Cheronet, Elizabeth Curtis, Olga Flegontova, Lora Iliev, Aisling Kearns, Denise Keating, Ann Marie Lawson, Matthew Mah, Adam Micco, Megan Michel, Jonas Oppenheimer, Lijun Qiu, J Noah Workman, Fatma Zalzala, Anna Szécsényi-Nagy, Pier Francesco Palamara, Swapan Mallick, Nadin Rohland, Ron Pinhasi, David Reich
The Yamnaya archaeological complex appeared around 3300BCE across the steppes north of the Black and Caspian Seas, and by 3000BCE reached its maximal extent from Hungary in the west to Kazakhstan in the east. To localize the ancestral and geographical origins of the Yamnaya among the diverse Eneolithic people that preceded them, we studied ancient DNA data from 428 individuals of which 299 are reported for the first time, demonstrating three previously unknown Eneolithic genetic clines. First, a "Caucasus-Lower Volga" (CLV) Cline suffused with Caucasus hunter-gatherer (CHG) ancestry extended between a Caucasus Neolithic southern end in Neolithic Armenia, and a steppe northern end in Berezhnovka in the Lower Volga...
April 18, 2024: bioRxiv
#8
JOURNAL ARTICLE
Guido Alberto Gnecchi-Ruscone, Zsófia Rácz, Levente Samu, Tamás Szeniczey, Norbert Faragó, Corina Knipper, Ronny Friedrich, Denisa Zlámalová, Luca Traverso, Salvatore Liccardo, Sandra Wabnitz, Divyaratan Popli, Ke Wang, Rita Radzeviciute, Bence Gulyás, István Koncz, Csilla Balogh, Gabriella M Lezsák, Viktor Mácsai, Magdalena M E Bunbury, Olga Spekker, Petrus le Roux, Anna Szécsényi-Nagy, Balázs Gusztáv Mende, Heidi Colleran, Tamás Hajdu, Patrick Geary, Walter Pohl, Tivadar Vida, Johannes Krause, Zuzana Hofmanová
From AD 567-568, at the onset of the Avar period, populations from the Eurasian Steppe settled in the Carpathian Basin for approximately 250 years1 . Extensive sampling for archaeogenomics (424 individuals) and isotopes, combined with archaeological, anthropological and historical contextualization of four Avar-period cemeteries, allowed for a detailed description of the genomic structure of these communities and their kinship and social practices. We present a set of large pedigrees, reconstructed using ancient DNA, spanning nine generations and comprising around 300 individuals...
April 24, 2024: Nature
#9
Michael Eisenstein
No abstract text is available yet for this article.
April 24, 2024: Nature
#10
Lara M Cassidy
No abstract text is available yet for this article.
April 24, 2024: Nature
#11
JOURNAL ARTICLE
Siyu Chai, Shuhua Li, Ruxin Zhu, Li Luo, Kaiqin Chen, Yinlei Lei, Weihong Wan, Xijie Hu, Shiquan Liu, Pengyu Chen
UNLABELLED: Short tandem repeats (STRs) are the most common genetic markers in forensic and human population genetics due to their high polymorphism, rapid detection, and reliable genotyping. To adapt the rapid growth of forensic DNA database and solve problems in disputed cases, a panel of 23 autosomal STR loci with high discriminating ability was constructed recently. The Tai-Kadai-speaking Gelao is the most ancient indigenous minority in Guizhou province, however, the forensic efficiency and population genetic structure remain poorly explored...
June 2024: Forensic Sciences Research
#12
Shilun Zhu, Zehui Chen, Songmei Hu, Weilin Wang, Peng Cao, Feng Liu, Qingyan Dai, Xiaotian Feng, Ruowei Yang, Wanjing Ping, Qiaomei Fu
No abstract text is available yet for this article.
April 2024: Journal of Genetics and Genomics
#13
JOURNAL ARTICLE
Qi Lin, Ke Zhang, Charline Giguet-Covex, Fabien Arnaud, Suzanne McGowan, Ludovic Gielly, Eric Capo, Shixin Huang, Gentile Francesco Ficetola, Ji Shen, John A Dearing, Michael E Meadows
Understanding the transient dynamics of interlinked social-ecological systems (SES) is imperative for assessing sustainability in the Anthropocene. However, how to identify critical transitions in real-world SES remains a formidable challenge. In this study, we present an evolutionary framework to characterize these dynamics over an extended historical timeline. Our approach leverages multidecadal rates of change in socioeconomic data, paleoenvironmental, and cutting-edge sedimentary ancient DNA records from China's Yangtze River Delta, one of the most densely populated and intensively modified landscapes on Earth...
April 23, 2024: Proceedings of the National Academy of Sciences of the United States of America
#14
JOURNAL ARTICLE
Zewen Sun, Lin Pan, Aowen Tian, Peng Chen
The prevalence of COVID-19 critical illness varies across ethnicities, with recent studies suggesting that genetic factors may contribute to this variation. The aim of this study was to investigate natural selection signals of genes associated with critically-ill COVID-19 in sub-Saharan Africans. Severe COVID-19 SNPs were obtained from the HGI website. Selection signals were assessed in 661 sub-Sahara Africans from 1000 Genomes Project using integrated haplotype score (iHS), cross-population extended haplotype homozygosity (XP-EHH), and fixation index (Fst)...
April 16, 2024: Infection, Genetics and Evolution
#15
JOURNAL ARTICLE
Pradeep Ruperao, Prasad Bajaj, Rashmi Yadav, Mahalingam Angamuthu, Rajkumar Subramani, Vandana Rai, Kapil Tiwari, Abhishek Rathore, Kuldeep Singh, Gyanendra Pratap Singh, Ulavappa B Angadi, Sean Mayes, Parimalan Rangan
Sesame (Sesamum indicum L.) is an ancient oilseed crop belonging to the family Pedaliaceae and a globally cultivated crop for its use as oil and food. In this study, 2496 sesame accessions, being conserved at the National Genebank of ICAR-National Bureau of Plant Genetic Resources (NBPGR), were genotyped using genomics-assisted double-digest restriction-associated DNA sequencing (ddRAD-seq) approach. A total of 64,910 filtered single-nucleotide polymorphisms (SNPs) were utilized to assess the genome-scale diversity...
April 17, 2024: Plant Genome
#16
JOURNAL ARTICLE
Prashant Ghimire, Catalina Palacios, Jeremiah Trimble, Sangeet Lamichhaney
The accessibility of genomic tools in evolutionary biology has allowed for a thorough exploration of various evolutionary processes associated with adaptation and speciation. However, genomic studies in natural systems present numerous challenges, reflecting the inherent complexities of studying organisms in their native habitats. The utilization of museum specimens for genomics research has received increased attention in recent times, facilitated by advancements in ancient DNA techniques. In this study, we have utilized a museum genomics approach to analyze historic specimens of Woolly-necked storks (Ciconia sps...
April 16, 2024: G3: Genes—Genomes—Genetics
#17
JOURNAL ARTICLE
Jiashuo Zhang, Xuebo Li, Liangliang Li, Anqi Chen, Suhua Zhang
The goal of the following study is to clarify whether the skeletal remains over 70 years old from missing persons and their alleged relatives shared identical Y-STR loci. Nowadays, advances in ancient DNA extraction techniques and approaches of using multiple different Y-STRs have significantly increased the possibility of obtaining DNA profiles from highly degraded skeletal remains. Given the ages and conditions of the skeletal remains, ancient DNA extraction methods can be used to maximize the probability of DNA recovery...
June 2024: Forensic Sciences Research
#18
JOURNAL ARTICLE
Renata C Ferreira, Camila R Rodrigues, James R Broach, Marcelo R S Briones
The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and archaic anatomically modern humans (AMHs). Although Neanderthal signatures are well documented in the nuclear genome, it has been proposed that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that modern human mitochondrial genomes contain 66 potential Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs), of which 36 lie in coding regions and 7 result in nonsynonymous changes...
March 28, 2024: International Journal of Molecular Sciences
#19
JOURNAL ARTICLE
Nozhat T Hassan, James D Galbraith, David L Adelson
Horizontal transfer of transposable elements (HTT) has been reported across many species and the impact of such events on genome structure and function has been well described. However, few studies have focused on reptilian genomes, especially HTT events in Testudines (turtles). Here, as a consequence of investigating the repetitive content of Malaclemys terrapin terrapin (Diamondback turtle) we found a high similarity DNA transposon, annotated in RepBase as hAT-6_XT, shared between other turtle species, ray-finned fishes, and a frog...
April 11, 2024: Mobile DNA
#20
JOURNAL ARTICLE
Cinthia C Abbona, Ophélie Lebrasseur, Francisco J Prevosti, Eva Peralta, Lucio González Venanzi, Laurent Frantz, Greger Larson, Adolfo F Gil, Gustavo A Neme
The southern Mendoza province, located in the northern region of Patagonia, was inhabited by hunter-gatherer groups until historic times. Previous archaeological studies have reported canid remains among faunal assemblages, which were assumed to be part of the human diet. However, the taxonomic identification and significance of these canids within human groups have raised questions. In this study, we used ancient DNA analysis, morphological examination and stable isotope analysis (δ13 Ccol and δ15 N) to re-evaluate the taxonomic assignment of a canid discovered at the Late Holocene burial site of Cañada Seca...
April 2024: Royal Society Open Science
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