Article
Biochemistry & Molecular Biology
Meline Saubin, Aurelien Tellier, Solenn Stoeckel, Axelle Andrieux, Fabien Halkett
Summary: Adaptation in natural populations can lead to rapid changes in phenotype and genotype frequencies over a few generations. A new ABC framework is proposed to understand the genetic and demographic changes during rapid adaptation. The framework demonstrates high accuracy in both model and parameter estimations and is applied to empirical data of a pathogen population. The inferred values are consistent with empirical knowledge, suggesting the potential of this framework in studying rapid adaptation.
Article
Biology
Khai C. Ang, Victor A. Canfield, Tiffany C. Foster, Thaddeus D. Harbaugh, Kathryn A. Early, Rachel L. Harter, Katherine P. Reid, Shou Ling Leong, Yuka Kawasawa, Dajiang Liu, John W. Hawley, Keith C. Cheng
Summary: This study focused on a Native American population with high Native American genetic ancestry, aiming to investigate the impact of this ancestry on skin color variation. The results showed that Native American genetic ancestry had the greatest effect on reducing skin pigmentation, while genetic mutations from European and African ancestries had smaller effects. However, the specific genetic variants responsible for light skin in Native American/East Asian populations remain to be identified.
Editorial Material
Multidisciplinary Sciences
Conrad O. Iyegbe, Paul F. O'Reilly
Summary: Rare and common genetic variants associated with schizophrenia provide convergent clues about the underlying biology of this complex disorder.
Article
Genetics & Heredity
Kevin Liao, Jedidiah Carlson, Sebastian Zollner
Summary: As next-generation sequencing technology has advanced, population genetics has had to adapt to the exponential increase in genetic data. One common approach to analyzing large sequencing data is through the allele frequency spectrum, but this approach assumes that different mutation types are interchangeable, which may not be the case due to spatial and temporal variation in forces such as mutation rate and biased gene conversion.
G3-GENES GENOMES GENETICS
(2023)
Editorial Material
Multidisciplinary Sciences
Samira Asgari, Lionel A. Pousaz
Summary: An individual's genetics play a role in their susceptibility to infectious diseases and the severity of symptoms. A recent international study has identified specific regions of the human genome that can impact the risk of severe COVID-19.
Article
Biochemistry & Molecular Biology
Nina Marchi, Adamandia Kapopoulou, Laurent Excoffier
Summary: This study examines the impact of sampling heterogeneity of modern and ancient genomes on demographic inference, and introduces a new approach to mitigate this issue. The study shows that the new structured method is efficient and relevant for handling scattered and ancient DNA samples.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Eric Wootton, Claude Robert, Jolle Taillon, Steeve Cote, Aaron B. A. Shafer
Summary: In this study, the relationships between measures of inbreeding, genomic constraint, and mutational load were investigated in white-tailed deer, caribou, and mountain goat. The results showed that mountain goats had higher inbreeding coefficients and more evolutionarily constrained regions compared to caribou and white-tailed deer. Additionally, white-tailed deer had the highest mutational load, followed by caribou, while mountain goats had the lowest.
Article
Biodiversity Conservation
Caroline Kebaili, Stephanie Sherpa, Maya Gueguen, Julien Renaud, Delphine Rioux, Laurence Despres
Summary: Climate is a major driver of species distributions, but different species respond differently to climate change. This study focuses on the ability of limited dispersal and habitat-specialist species to track climate change at a local scale. The genetic and demographic impacts of past climate cycles are compared in three butterfly species in the Jura massif. The study finds similarities in thermal niche and population histories, but no correlation between changes in suitable areas and population size. This suggests that species ranges moved beyond the study area during unfavorable climatic periods, and habitat loss and deterioration are major drivers of the species' decline.
BIOLOGICAL CONSERVATION
(2023)
Article
Multidisciplinary Sciences
Gabriela Franca Oliveira, Ana Carolina Campana Nascimento, Camila Ferreira Azevedo, Mauricio de Oliveira Celeri, Lais Mayara Azevedo Barroso, Isabela de Castro Sant'Anna, Jose Marcelo Soriano Viana, Marcos Deon Vilela de Resende, Moyses Nascimento
Summary: The study aimed to evaluate the performance of Quantile Regression (QR) in Genome-Wide Association Studies (GWAS) for detecting QTLs associated with phenotypic traits. Simulated data was used with traits of different heritability levels and controlled by different numbers of QTLs. QR models showed higher detection power and lower false positive rate compared to the General Linear Model (GLM). QR had a high detection power in scenarios with low heritability and can effectively detect QTLs even with a small number of individuals.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Hideki Innan, Takahiro Sakamoto
Summary: Diffusion theory is commonly used in describing allele frequency behavior in one-locus one-population models, but handling it in models with multiple loci or populations is challenging. Multi-dimensional diffusion equations have shown strong potential in addressing evolutionary questions in population genetics.
PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES
(2021)
News Item
Multidisciplinary Sciences
Roxanne Khamsi
Summary: Researchers are working on building a human 'pangenome' to represent the entirety of human genetic variation, but not everyone is ready to participate in this project.
Article
Plant Sciences
Tam Minh Nguyen, Duy Dinh Vu, Hien Phan Dang, Xuan Thi Tuyet Bui, Hong Phan Lan Nguyen, Duc Minh Nguyen
Summary: Moderate levels of genetic diversity and differentiation were found in Anisoptera costata. Population divergence during the Younger Dryas was detected. The anthropogenic disturbance significantly impacted the genetic diversity of the species in low tropical forests.
Article
Biochemistry & Molecular Biology
Alessio Iannucci, Andrea Benazzo, Chiara Natali, Evy Ayu Arida, Moch Samsul Arifin Zein, Tim S. Jessop, Giorgio Bertorelle, Claudio Ciofi
Summary: Population and conservation genetics studies of the Komodo dragon using whole-genome sequencing of 24 individuals revealed three main genomic groups, with populations on Komodo Island and the northern coast of Flores identified as distinct conservation units. The genomic divergence among island populations was interpreted as related to changes in sea level affecting connectivity. Demographic inference indicated a steep population decline in Komodo dragons over the last million years, reaching a stable N-e during the Saalian glacial cycle before a rapid decrease. Genomic diversity of Komodo dragons was similar to that of endangered or extinct reptile species, highlighting the importance of whole-genome analysis in defining population structure and demographic dynamics for conservation efforts.
Article
Biochemistry & Molecular Biology
Inger Skrede, Claude Murat, Jaqueline Hess, Sundy Maurice, Jorn Henrik Sonstebo, Annegret Kohler, Dominique Barry-Etienne, Dan Eastwood, Nils Hogberg, Francis Martin, Havard Kauserud
Summary: Research shows that the populations of dry rot fungus in Europe and Japan split 3000-19,000 years ago, with the European population experiencing a tight bottleneck approximately 250 generations ago, leading to low adaptive potential. Only two loci under selection were found, and selective sweep analyses revealed different gene signals in Japan and Europe.
Article
Cardiac & Cardiovascular Systems
Ray E. Hershberger, Jason Cowan, Elizabeth Jordan, Daniel D. Kinnamon
Summary: Insights into the genetic architecture of dilated cardiomyopathy (DCM) are rapidly evolving, showing a complex and diverse nature. In addition to monogenic structures, oligogenic basis, rare variants, low-frequency, and common genetic variations may contribute to the complexity of DCM, along with gene-environment interactions.
CIRCULATION RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Raphael T. F. Coimbra, Sven Winter, Vikas Kumar, Klaus-Peter Koepfli, Rebecca M. Gooley, Pavel Dobrynin, Julian Fennessy, Axel Janke
Summary: The taxonomy of giraffes has been disputed, with early classifications recognizing only one species with nine subspecies, but recent genomic studies suggesting at least four species. Population structure and phylogenomic analyses revealed four independently evolving giraffe lineages, supporting the recognition of four species and seven subspecies, emphasizing the importance of achieving consensus for assessing threat levels and improving conservation efforts.
Article
Genetics & Heredity
Sofiia Kolchanova, Alexey Komissarov, Sergei Kliver, Anyi Mazo-Vargas, Yashira Afanador, Jafet Velez-Valentin, Ricardo Valentin de la Rosa, Stephanie Castro-Marquez, Israel Rivera-Colon, Audrey J. Majeske, Walter W. Wolfsberger, Taylor Hans, Andre Corvelo, Juan-Carlos Martinez-Cruzado, Travis C. Glenn, Orlando Robinson, Klaus-Peter Koepfli, Taras K. Oleksyk
Summary: This study sequenced and annotated full mitochondrial genomes of Amazon parrots from the Greater Antilles, revealing the lowest sequence diversity in the population of A. vittata in Puerto Rico. The results support a stepping-stone dispersal and speciation hypothesis, contributing to the understanding of evolutionary history and guiding future conservation efforts in the Caribbean.
Article
Optics
Nikita Ustimenko, Kseniia Baryshnikova, Roman Melnikov, Danil Kornovan, Vladimir Ulyantsev, Boris N. Chichkov, Andrey B. Evlyukhin
Summary: The study investigated the applicability of the coupled multipole model for modeling light focusing by finite-size nanostructures of silicon nanospheres, and showed strong optimization potential for designing ultrathin metalenses using an evolutionary algorithm. The results were verified by numerical simulations and demonstrated through comparison with analytical approximations.
JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS
(2021)
Article
Evolutionary Biology
Marina Alvarez-Estape, Claudia Fontsere, Aitor Serres-Armero, Lukas F. K. Kuderna, Pavel Dobrynin, Hela Guidara, Budhan S. Pukazhenthi, Klaus-Peter Koepfli, Tomas Marques-Bonet, Eulalia Moreno, Esther Lizano
Summary: The study demonstrates that captive breeding programmes can serve as source populations for future reintroductions of threatened species, and genomics can play a crucial role in conservation plans.
EVOLUTIONARY APPLICATIONS
(2022)
Review
Zoology
M. Krofel, J. Hatlauf, W. Bogdanowicz, L. A. D. Campbell, R. Godinho, Y. V. Jhala, A. C. Kitchener, K. -P. Koepfli, P. Moehlman, H. Senn, C. Sillero-Zubiri, S. Viranta, G. Werhahn, F. Alvares
Summary: Successful conservation relies on accurate taxonomy, which is currently unstable for canids in Africa, Eurasia, and Australasia. Recent molecular and morphological studies challenge earlier classifications, particularly for African jackals, Asian wolves, and Australasian dogs. Major knowledge gaps exist, recommendations for future research are provided, and an updated taxonomic framework is proposed based on molecular data, morphology, biogeography, and behavioral ecology.
JOURNAL OF ZOOLOGY
(2022)
Article
Physics, Multidisciplinary
Daria Zvyagintseva, Helgi Sigurdsson, Valerii K. Kozin, Ivan Iorsh, Ivan A. Shelykh, Vladimir Ulyantsev, Oleksandr Kyriienko
Summary: In this study, an unsupervised machine learning approach is used to map the phases of a polariton condensate lattice and classify unique polarization patterns. By applying machine learning methods, we can gain a better understanding of the non-equilibrium nature of exciton-polariton condensates and the qualitative changes in their steady states.
COMMUNICATIONS PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Lorena Derezanin, Asta Blazyte, Pavel Dobrynin, David A. Duchene, Jose Horacio Grau, Sungwon Jeon, Sergei Kliver, Klaus-Peter Koepfli, Dorina Meneghini, Michaela Preick, Andrey Tomarovsky, Azamat Totikov, Joerns Fickel, Daniel W. Forster
Summary: Species of the mustelid subfamily Guloninae have diverse adaptations in feeding ecologies, reproductive strategies, and morphology. By comparing the genomes of different species, we identified multiple candidate loci associated with traits such as diet, body condition, and reproduction. Our study highlights the importance of considering various types of genomic variations in the identification of adaptive loci.
Article
Genetics & Heredity
Ekaterina A. Gibitova, Pavel Dobrynin, Ekaterina A. Pomerantseva, Elizaveta Musatova, Anna Kostareva, Igor Evsyukov, Sergey Y. Rychkov, Olga Zhukova, Oxana Y. Naumova, Elena L. Grigorenko
Summary: This study presents new data on whole-exome sequencing of children with autistic spectrum disorders (ASD) from an understudied Russian population. The findings reveal potential ASD candidate-variants and a high prevalence of common ASD-associated genomic variants.
Article
Evolutionary Biology
Osman Ibis, Klaus-Peter Koepfli, Servet Ozcan, Coskun Tez
Summary: Crocidura, the genus with the most species in mammals, was analyzed in this study. The analysis revealed that the Turkish shrews were divided into three major lineages, and proposed the existence of new taxonomic units and possible refugia.
ORGANISMS DIVERSITY & EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Elisabeth Hempel, Faysal Bibi, J. Tyler Faith, Klaus-Peter Koepfli, Achim M. Klittich, David A. Duchene, James S. Brink, Daniela C. Kalthoff, Love Dalen, Michael Hofreiter, Michael Westbury
Summary: The blue antelope, the only large African mammal species to have become extinct in historical times, lacks nuclear genomic information. Recent research shows that many alleged blue antelope museum specimens are actually roan or sable antelopes, further limiting the availability of genomic information for this extinct species. However, draft genomes of the blue antelope have been recovered from a historical specimen and a fossil specimen, making it the oldest paleogenome from Africa. Phylogenomic analyses confirm that blue and sable antelope are sister species and reveal ancient gene flow from roan to blue antelope. The lower genomic diversity of the blue antelope compared to other antelope species suggests a small population size since at least the early Holocene. The species continued to persist in the Holocene, indicating that human impact during the colonial era likely played a decisive role in its extinction.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Graham Gower, Aaron P. Ragsdale, Gertjan Bisschop, Ryan N. Gutenkunst, Matthew Hartfield, Ekaterina Noskova, Stephan Schiffels, Travis J. Struck, Jerome Kelleher, Kevin R. Thornton
Summary: Understanding the demographic history of populations is crucial in population genetics, but the lack of a standardized format to define population dynamic models hampers progress in the field. Therefore, we propose the Demes data model and file format to address these issues.
Article
Biochemistry & Molecular Biology
Natacha Nikolic, Floriaan Devloo-Delva, Diane Bailleul, Ekaterina Noskova, Clement Rougeux, Chrystelle Delord, Philippe Borsa, Cathy Liautard-Haag, Mohamad Hassan, Amandine D. Marie, Pierre Feutry, Peter Grewe, Campbell Davies, Jessica Farley, Daniel Fernando, Sebastian Biton-Porsmoguer, Francois Poisson, Denham Parker, Agostino Leone, Jorden Aulich, Matt Lansdell, Francis Marsac, Sophie Arnaud-Haond
Summary: The blue shark is a widely distributed top predator, classified as Critically Endangered in the Mediterranean Sea and Near Threatened globally. Genetic studies have previously suggested a single global population. However, this study used a genome-wide approach and revealed two main groups, the Mediterranean Sea and northern Atlantic samples differentiated from Indo-west Pacific samples. Within the Atlantic Ocean, further genetic differentiation was observed, as well as between the Atlantic Ocean and the Mediterranean Sea. The results highlight the importance of considering genetic population structure and demographic history in the management and conservation strategies of the blue shark.
Article
Multidisciplinary Sciences
Emily Humble, Martin A. Stoffel, Kara Dicks, Alex D. Ball, Rebecca M. Gooley, Justin Chuven, Ricardo Pusey, Mohammed Al Remeithi, Klaus-Peter Koepfli, Budhan Pukazhenthi, Helen Senn, Rob Ogden
Summary: In an era of habitat loss and overexploitation, small populations face the effects of isolation and inbreeding. Genetic management is vital for their survival. This study shows that unmanaged populations have higher inbreeding coefficients and more deleterious genotypes compared to managed populations. The findings highlight the risks of inbreeding and emphasize the importance of maintaining genetic diversity in vulnerable populations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Ekaterina Noskova, Viacheslav Borovitskiy
Summary: In population genetics, inferring demographic histories of species and populations is a central problem, often approached as an optimization problem to maximize log-likelihood by finding optimal model parameters. However, the evaluation of log-likelihoods is expensive, particularly for larger populations. This study introduces a new optimization pipeline based on Bayesian optimization, which outperforms the widely used genetic algorithm solution in the limited time budget setting with four and five populations.
G3-GENES GENOMES GENETICS
(2023)
Article
Microbiology
Evgenii I. I. Olekhnovich, Artem B. B. Ivanov, Anna A. A. Babkina, Arseniy A. A. Sokolov, Vladimir I. I. Ulyantsev, Dmitry E. E. Fedorov, Elena N. N. Ilina
Summary: In this study, a list of potentially beneficial bacteria associated with melanoma immunotherapy responsiveness was compiled. Functional biomarkers of immunotherapy responsiveness were also identified and found to be dispersed among different bacterial species. These findings contribute to understanding the relationship between gut microbiome composition and treatment response, and have implications for the development of diagnostic tests and recommendations for gut microbiome correction in cancer immunotherapy.
