Article
Multidisciplinary Sciences
Harry A. Thorpe, Elise Tourrette, Koji Yahara, Filipa F. Vale, Siqi Liu, Monica Oleastro, Teresa Alarcon, Tsachi-Tsadok Perets, Saeid Latifi-Navid, Yoshio Yamaoka, Beatriz Martinez-Gonzalez, Ioannis Karayiannis, Timokratis Karamitros, Dionyssios N. Sgouras, Wael Elamin, Ben Pascoe, Samuel K. Sheppard, Jukka Ronkainen, Pertti Aro, Lars Engstrand, Lars Agreus, Sebastian Suerbaum, Kaisa Thorell, Daniel Falush
Summary: Helicobacter pylori has recently spread out of Africa, replacing deleterious variants that accumulated during the original out of Africa migrations more than 50,000 years ago.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Francesco Montinaro, Vasili Pankratov, Burak Yelmen, Luca Pagani, Mayukh Mondal
Summary: The study supports a back to Africa migration model over a single out of Africa model, with two sequential separations between African and out of African populations around 60-90 thousand years ago, separated by 13-15 thousand years.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
Domingo Rivera, Javier Balbontin, Sergio Perez Gil, Jose Maria Abad Gomez-Pantoja, Juan Jose Negro
Summary: This study examines the juvenile dispersal of the poorly studied Black-shouldered Kite in southwestern Spain and provides evidence supporting the Resources Competition Hypothesis. The study also analyzes the dispersal distance of the juveniles and provides crucial demographic parameters for future conservation plans.
Article
Multidisciplinary Sciences
Mahmoud Abbas, Zhongping Lai, John D. Jansen, Hua Tu, Mohammad Alqudah, Xiaolin Xu, Bety S. Al-Saqarat, Mu'ayyad Al Hseinat, Xianjiao Ou, Michael D. Petraglia, Paul A. Carling
Summary: Based on luminescence dating of wetland sediments, we found evidence of prolonged moisture availability in the southern Levant during the last interglaciation. This suggests that the region could have served as a well-watered corridor, funneling migrants into western Asia and northern Arabia.
Article
Biochemistry & Molecular Biology
Thibault Latrille, Vincent Lanore, Nicolas Lartillot
Summary: Mutation-selection phylogenetic codon models are a principled approach for studying the interplay between mutation, selection, and drift, but their assumption of constant genetic drift is unrealistic. By introducing variation in effective population size and mutation rate between lineages, the model can better account for the joint evolutionary process of these lineage-specific variables. The model, tested on simulated and empirical data, suggests reasonable reconstructions of evolutionary trends, although potential issues with assumptions about epistatic interactions between sites remain.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Ecology
Krystyna Nadachowska-Brzyska, Mateusz Konczal, Wieslaw Babik
Summary: Effective population size (Ne) is a key evolutionary parameter that determines genetic variation levels and selection efficacy. Ne estimation and interpretation are essential in evolutionary and conservation biology, with diverse applications and methods available. Recent advancements in estimating temporal Ne trends provide a comprehensive understanding of the evolutionary continuum.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Nils Ryman, Linda Laikre, Ola Hossjer
Summary: Measurement of allele frequency shifts between temporally spaced samples has been used to estimate effective population size (N-e), also known as variance effective size (N-eV). Our study reveals that N-eV of a local population within a sub-structured population is influenced by genetic drift, migration rate (m), and census size (N-c). The relationship between N-e and N-c determines whether the realized N-eV of a local population increases or decreases with increasing m. The effect of N-c on N-eV is most significant at higher migration rates.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Chemistry, Organic
Wataru Setaka, Yuto Ikeda, Yusuke Inagaki, Kazuaki Ohara, Kentaro Yamaguchi
Summary: In large bicycloalkanes, the stability of different in/out forms depends on the size of the cage. The smaller derivatives favor the in/out form, while the larger derivatives prefer the twist-out/out form due to dispersion forces.
Article
Biochemistry & Molecular Biology
Irene Novo, Noelia Perez-Pereira, Enrique Santiago, Humberto Quesada, Armando Caballero
Summary: The availability of high-density markers allows the estimation of historical effective population size. Recent refinement methods have been shown to be accurate with simulation data and have been applied to real data of various species. An experimental design with Drosophila melanogaster was carried out to test the method, which showed generally good performance. The limitations of the method and its application were discussed.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Multidisciplinary Sciences
Raquel Viana, Sikhulile Moyo, Daniel G. Amoako, Houriiyah Tegally, Cathrine Scheepers, Christian L. Althaus, Ugochukwu J. Anyaneji, Phillip A. Bester, Maciej F. Boni, Mohammed Chand, Wonderful T. Choga, Rachel Colquhoun, Michaela Davids, Koen Deforche, Deelan Doolabh, Louis du Plessis, Susan Engelbrecht, Josie Everatt, Jennifer Giandhari, Marta Giovanetti, Diana Hardie, Verity Hill, Nei-Yuan Hsiao, Arash Iranzadeh, Arshad Ismail, Charity Joseph, Rageema Joseph, Legodile Koopile, Sergei L. Kosakovsky Pond, Moritz U. G. Kraemer, Lesego Kuate-Lere, Oluwakemi Laguda-Akingba, Onalethatha Lesetedi-Mafoko, Richard J. Lessells, Lockman, Alexander G. Lucaci, Arisha Maharaj, Boitshoko Mahlangu, Tongai Maponga, Kamela Mahlakwane, Zinhle Makatini, Gert Marais, Dorcas Maruapula, Kereng Masupu, Mogomotsi Matshaba, Simnikiwe Mayaphi, Nokuzola Mbhele, Mpaphi B. Mbulawa, Adriano Mendes, Koleka Mlisana, Anele Mnguni, Thabo Mohale, Monika Moir, Kgomotso Moruisi, Mosepele Mosepele, Gerald Motsatsi, Modisa S. Motswaledi, Thongbotho Mphoyakgosi, Nokukhanya Msomi, Peter N. Mwangi, Yeshnee Naidoo, Noxolo Ntuli, Martin Nyaga, Lucier Olubayo, Sureshnee Pillay, Botshelo Radibe, Yajna Ramphal, Upasana Ramphal, James E. San, Lesley Scott, Roger Shapiro, Lavanya Singh, Pamela Smith-Lawrence, Wendy Stevens, Amy Strydom, Kathleen Subramoney, Naume Tebeila, Derek Tshiabuila, Joseph Tsui, Stephanie van Wyk, Steven Weaver, Constantinos K. Wibmer, Eduan Wilkinson, Nicole Wolter, Alexander E. Zarebski, Boitumelo Zuze, Dominique Goedhals, Wolfgang Preiser, Florette Treurnicht, Marietje Venter, Carolyn Williamson, Oliver G. Pybus, Jinal Bhiman, Allison Glass, Darren P. Martin, Andrew Rambaut, Simani Gaseitsiwe, Anne von Gottberg, Tulio de Oliveira
Summary: The SARS-CoV-2 epidemic in southern Africa has experienced three distinct waves, driven by different variants. The recently identified Omicron variant has rapidly spread in South Africa and to numerous countries, raising global concern.
Article
Genetics & Heredity
Ayman A. Hussein, Reem Hamad, Melanie J. Newport, Muntaser E. Ibrahim
Summary: Personalized, stratified or precision approaches aim to put individual variation at the center of scientific medicine, using genomic and biomarker information to predict disease risk and treatment response. However, these approaches overlook the hierarchical nature of human variation and the importance of population differences.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Sophie B. Cowling, Pracha Treeintong, John Ferguson, Hamidreza Soltani, Ranjan Swarup, Sean Mayes, Erik H. Murchie
Summary: African rice (Oryza glaberrima) exhibits extensive natural variation in photosynthetic traits, photoprotection, and stomatal conductance. These dynamic traits are important for the adaptation of O. glaberrima to diverse African environments and have value for gene discovery and crop improvement.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Enrique Santiago, Armando Caballero, Carlos Kopke, Irene Novo
Summary: A new method is developed to estimate the contemporary effective population size (Ne) based on linkage disequilibrium (LD) in non-model species. It can be applied to different mating systems and variations in family size distribution. The method uses an artificial neural network to predict confidence intervals, providing more consistent estimates.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Gordon Luikart, Tiago Antao, Brian K. Hand, Clint C. Muhlfeld, Matthew C. Boyer, Ted Cosart, Brian Trethewey, Robert Al-Chockhachy, Robin S. Waples
Summary: Estimating the effective population size and effective number of breeders per year using computer simulations showed a bias of 5%-10% when using SNPs or microsatellites across different species. However, precision was higher for SNPs than for microsatellites, and confidence intervals were narrow enough to achieve high statistical power in rejecting null hypotheses for different true values of N-b and sample sizes.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Agriculture, Dairy & Animal Science
Irene Novo, Pilar Ordas, Natalia Moraga, Enrique Santiago, Humberto Quesada, Armando Caballero
Summary: The estimation of historical Ne provided by the software GONE can be substantially biased by recent mixture of populations, low rates of continued migration, and high frequencies of chromosomal inversions. Population structure analyses and restriction of estimation to differentiated groups can help mitigate biases. Removing genomic regions involved in inversions can also improve the accuracy of Ne estimates.
GENETICS SELECTION EVOLUTION
(2023)
Article
Zoology
Flavia R. Miranda, Guilherme S. T. Garbino, Fabio A. Machado, Fernando A. Perini, Fabricio R. Santos, Daniel M. Casali
Summary: A taxonomic revision of maned sloths revealed the presence of two species: the northern maned sloth and the southern maned sloth. These species diverged in the Early Pliocene and are distributed allopatrically. The conservation status of both species needs to be reassessed.
JOURNAL OF MAMMALOGY
(2023)
Article
Oncology
Queralt Serra-Camprubi, Helena Verdaguer, Winona Oliveros, Nuria Lupion-Garcia, Alba Llop-Guevara, Cristina Molina, Maria Vila-Casadesus, Anthony Turpin, Cindy Neuzillet, Joan Frigola, Jessica Querol, Mariana Yanez-Bartolome, Florian Castet, Carles Fabregat-Franco, Carmen Escudero-Iriarte, Marta Escorihuela, Enrique J. Arenas, Cristina Bernado-Morales, Noemi Haro, Francis J. Giles, Oscar J. Pozo, Josep M. Miquel, Paolo G. Nuciforo, Ana Vivancos, Marta Mele, Violeta Serra, Joaquim Arribas, Josep Tabernero, Sandra Peiro, Teresa Macarulla, Tian Tian
Summary: It has been found that advanced cholangiocarcinoma patients with BRCA2 gene mutations are likely to benefit from PARP inhibitor therapy, while those with mutations in IDH1, ARID1A, or BAP1 will not. The patient-derived xenograft models provide new opportunities for evaluating drug response and prioritizing clinical trials.
CLINICAL CANCER RESEARCH
(2023)
Article
Evolutionary Biology
Laura Vila-Valls, Julen Aizpurua-Iraola, Sebastian Casinge, Karin Bojs, Andre Flores-Bello, Neus Font-Porterias, David Comas
Summary: The Resande are a minority ethnic group in Sweden, believed to be a mixture of Swedish and Romani populations. Through analyzing genome-wide data, researchers have confirmed the Romani-related ancestry of the Resande and identified an admixture event between Romani-like and Swedish-like populations occurring between the mid-18th and mid-19th centuries. This study sheds light on the origins and demographic history of the Resande from a genetic perspective.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Marcel Lucas-Sanchez, Karima Fadhlaoui-Zid, David Comas
Summary: This study confirms the genetic influence of trans-Saharan migrations in present-day North Africa and provides new evidence about its quantity, geographical origin, and dates. The findings highlight the significance of trans-Saharan human genetic contacts and contribute to understanding the genomic composition of North Africa.
Article
Biochemistry & Molecular Biology
Sibelle T. Vilaca, Francesco Maroso, Paulo Lara, Benoit de Thoisy, Damien Chevallier, Larissa Souza Arantes, Fabricio R. Santos, Giorgio Bertorelle, Camila J. Mazzoni
Summary: Hybridization and introgression patterns in the Brazilian sea turtle population were investigated using RAD-Seq markers, mitogenomes, and satellite telemetry. The study found that all adult hybrids were first generation (F1) and most displayed loggerhead migratory behavior. Paternal leakage and different proportions of mitochondria from maternal and paternal species were also detected.
Article
Genetics & Heredity
Jose R. Sandoval, Susana Revollo, Cinthia Cuellar, Daniela R. Lacerda, Marilza S. Jota, Ricardo Fujita, Fabricio R. Santos
Summary: During the colonial period in South America, the genetic makeup of autochthonous populations was impacted and reconfigured due to relocation by European missionary reductions and other factors. This study used DNA comparison studies to explore the genetic relationships among Takanan and Panoan-speaking peoples in the Amazonian areas of Peru, Bolivia, and Brazil. The results revealed a shared ancestry between these groups, consistent with linguistic evidence and indicating an early Arawak expansion in the western Amazonia.
ANNALS OF HUMAN GENETICS
(2023)
Article
Genetics & Heredity
Julen Aizpurua-Iraola, Raquel Rasal, Lourdes Prieto, David Comas, Nuria Bonet, Ferran Casals, Francesc Calafell, Patricia Vasquez
Summary: The first nationwide forensic-quality complete mitogenome database of El Salvador was established, containing 334 samples. The study found 293 different haplotypes belonging to 54 different haplogroups, with 91% of them being of Native American origin. The database aims to serve as a basis for the identification of people who disappeared during or after the civil war.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
Article
Genetics & Heredity
Marco Antinucci, David Comas, Francesc Calafell
Summary: In this study, we conducted the first whole genome Copy Number Variant (CNV) study of the Roma population and compared them with reference populations from South Asia, the Middle East, and Europe. Using CNV calling software, we identified a total of 3171 deletions and 489 duplications. The analysis revealed that the patterns of deletion variation in the Roma population were consistent with those observed in single nucleotide polymorphisms (SNPs), indicating the influence of population history on CNV variation. Additionally, we found an increase in intronic deletions within Loss of Function (LoF)-intolerant genes, which may be attributed to reduced effective population size and slightly relaxed natural selection.
Article
Multidisciplinary Sciences
Caina M. Couto-Silva, Kelly Nunes, Gabriela Venturini, Marcos Araujo Castro e Silva, Lygia Pereira, David Comas, Alexandre Pereira, Tabita Hunemeier
Summary: Ecological conditions in the Amazon rainforests favor the transmission of tropical diseases, and the genetic adaptation of humans in this complex ecosystem is still unclear. This study analyzed the genomic data of 19 native populations to investigate the possible genetic adaptation to the Amazon rainforest. The results showed strong natural selection in genes related to Trypanosoma cruzi infection, the pathogen responsible for Chagas disease, a neglected tropical parasitic disease spreading worldwide.
Article
Ecology
Vanessa Villalba-Mouco, Marieke S. van de Loosdrecht, Adam B. Rohrlach, Helen Fewlass, Sahra Talamo, He Yu, Franziska Aron, Carles Lalueza-Fox, Lidia Cabello, Pedro Cantalejo Duarte, Jose Ramos-Munoz, Cosimo Posth, Johannes Krause, Gerd-Christian Weniger, Wolfgang Haak
Summary: During the Last Glacial Maximum, human populations experienced range contractions that had significant effects on their genetic variation. The genetic ancestry of individuals associated with the post-LGM Magdalenian technocomplex has been linked to pre-LGM Aurignacian groups, but differs from that of the Gravettian in central Europe. Genomic data from southern Spain indicates a direct connection between earlier Aurignacian-associated individuals and post-LGM Magdalenian-associated ancestry, suggesting Iberia as a potential refugium for western European pre-LGM ancestry.
NATURE ECOLOGY & EVOLUTION
(2023)
Editorial Material
Geology
James S. Crampton, Richard Jongens, Alan Cooper
NEW ZEALAND JOURNAL OF GEOLOGY AND GEOPHYSICS
(2023)
Article
Microbiology
Cody E. E. Parker, Alina N. N. Hiss, Maria A. A. Spyrou, Gunnar U. U. Neumann, Philip Slavin, Elizabeth A. A. Nelson, Sarah Nagel, Xandra Dalidowski, Susanne Friederich, Johannes Krause, Alexander Herbig, Wolfgang Haak, Kirsten I. I. Bos
Summary: The study finds strong evidence supporting the post-Black Death evolution of the pathogen within Europe, suggesting that the plague outbreaks after the Black Death originated locally rather than being reintroduced from outside.
Article
Peripheral Vascular Disease
Cynthia Al Hageh, Stephanie Chacar, Michella Ghassibe-Sabbagh, Daniel E. Platt, Andreas Henschel, Hamdan Hamdan, Dominique Gauguier, Yara El Murr, Eman Alefishat, Elie Chammas, Siobhan O'Sullivan, Antoine Abchee, Moni Nader, Pierre A. Zalloua
Summary: This study investigates the correlation between high Lp(a) levels and the degree of coronary artery stenosis. The results show that Lp(a) is a risk factor for coronary artery disease (CAD), especially in patients with HDL-cholesterol >= 35 mg/dL and non-obese patients. The study also finds a large proportion of patients with elevated Lp(a) levels had CAD, and the variant (rs1084651) of the LPA gene is significantly associated with CAD.
VASCULAR HEALTH AND RISK MANAGEMENT
(2023)
Article
Archaeology
Anna L. Gosling, Edana Lord, James Boocock, Sophia Cameron-Christie, K. Ann Horsburgh, Olga Kardailsky, Stefan Prost, Stephen Wilcox, David Addison, Adam Thompson, John Kalolo, Andrew C. Clarke, Elizabeth A. Matisoo-Smith
Summary: This study compares the genomic data of the current population and ancient individuals from Tokelau, finding less genetic diversity compared to other Polynesian populations. Rare mitochondrial lineages suggest prehistoric settlement by people from the northwest. Ancient DNA data supports the previous population abandonment and resettlement on Atafu, the northernmost atoll of Tokelau, from a population of Samoan or Samoan-origin. The study also reveals links between Tokelau and other atoll populations in the western Pacific.
JOURNAL OF ISLAND & COASTAL ARCHAEOLOGY
(2023)