Article
Biochemistry & Molecular Biology
Gaspard Kerner, Jeremy Choin, Lluis Quintana-Murci
Summary: Paleogenomics can be used as a tool for drug development by uncovering the genetic basis of modern diseases, such as inborn errors of immunity that affect the response to infections.
Article
Biochemistry & Molecular Biology
Yun-Hua Lo, Hsueh-Chien Cheng, Chia-Ni Hsiung, Show-Ling Yang, Han-Yu Wang, Chia-Wei Peng, Chun-Yu Chen, Kung-Ping Lin, Mei-Ling Kang, Chien-Hsiun Chen, Hou-Wei Chu, Chiao-Feng Lin, Mei-Hsuan Lee, Quintin Liu, Yoko Satta, Cheng-Jui Lin, Marie Lin, Shu-Miaw Chaw, Jun-Hun Loo, Chen-Yang Shen, Wen-Ya Ko
Summary: The study identified four major genetic ancestries among the Taiwanese Han population with signs of population mixture contributing to their genomes. Additionally, 16 candidate loci affected by positive natural selection were pinpointed, with five single genes showing significant associations with metabolic traits. This research provides critical insights into the evolutionary history and adaptation of the Taiwanese Han population.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Xinjun Zhang, Kelsey E. Witt, Mayra M. Banuelos, Amy Ko, Kai Yuan, Shuhua Xu, Rasmus Nielsen, Emilia Huerta-Sanchez
Summary: Recent studies indicate that interbreeding with archaic hominins was significant in aiding biological adaptations to new environments. For example, interbreeding with Denisovans helped Tibetan populations adapt to high-altitude environments. East Asian populations, despite their geographic proximity to the Denisova Cave, do not possess as much Denisovan ancestry as Melanesian populations. Two independent waves of Denisovan admixture into East Asians have been proposed, with one also shared with South Asians and Oceanians. The EPAS1 gene shows strong signs of selection and introgression from Denisovans, with one introgression event unique to East Asians introducing a beneficial haplotype into the ancestral Tibetan population.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Genetics & Heredity
Xiang Luo, Huijuan Zhou, Da Cao, Feng Yan, Pengpeng Chen, Jiangtao Wang, Keith Woeste, Xin Chen, Zhangjun Fei, Hong An, Maria Malvolti, Kai Ma, Chaobin Liu, Aziz Ebrahimi, Chengkui Qiao, Hang Ye, Mengdi Li, Zhenhua Lu, Jiabao Xu, Shangying Cao, Peng Zhao
Summary: In this study, the authors sequenced 309 walnut accessions from around the world, aiming to better understand the genetic diversity, domestication, and selection footprints in Persian walnuts. The results revealed core areas of genetic diversity and identified transcription factors related to nut diaphragm thickness that were under selection during domestication. This study provides valuable insights for the genomics-assisted breeding of this economically important crop.
Article
Ecology
Prabodh Kumar Bajpai, Arye Harel, Sharoni Shafir, Oz Barazani
Summary: This study explored ecotypic differentiation in populations of Eruca sativa from arid and Mediterranean habitats at the genomic level. The results showed that climatic conditions significantly influenced genetic diversity, and genes related to transcription factors and phytohormone signaling played a crucial role in adaptation to both abiotic and biotic conditions.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Seyi Fridaius Ulrich Vanvanhossou, Tong Yin, Carsten Scheper, Ruedi Fries, Luc Hippolyte Dossa, Sven Koenig
Summary: The Dwarf Lagune and the Savannah Somba cattle in Benin represent the endangered West African indigenous Shorthorn taurine, facing pressures from demographic, economic, and environmental factors. Genetic analysis revealed varying levels of admixture and selection signatures in these breeds, reflecting their unique genetic characteristics and breeding histories.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Richard Ian Bailey
Summary: Admixture is a widespread phenomenon and genomic studies can help us understand its impacts on evolution and speciation. Geographic and genomic cline analysis can provide evidence for reproductive isolation, selection, and adaptive introgression. The gghybrid package is a flexible Bayesian estimation tool for hybrid index and genomic clines, suitable for both small and large datasets. Simulations show that model comparison with waic is preferred, while the use of Bayesian posterior distributions and p values to select non-null loci should be avoided.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Kwondo Kim, Donghee Kim, Olivier Hanotte, Charles Lee, Heebal Kim, Choongwon Jeong
Summary: Present-day African cattle have a unique genetic profile resulting from a mixture of Bos taurus and Bos indicus populations. Research suggests that the earliest domestic cattle in Africa likely had a significant contribution from an extinct African aurochs lineage, and the indicine ancestry of African cattle is closely related to both North Indian and Southeast Asian indicine breeds.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biology
Taehyung Kwon, Kwondo Kim, Kelsey Caetano-Anolles, Samsun Sung, Seoae Cho, Choongwon Jeong, Olivier Hanotte, Heebal Kim
Summary: Our study confirms the genotype discrepancy between mitochondrial and nuclear genome in African admixed cattle. We propose a novel hypothesis of selection induced by mitonuclear incompatibility to explain this discrepancy, and our results support the role of male-biased B. indicus introgression and selection induced by mitonuclear incompatibility in shaping the current genomic status of African admixed cattle. We also identified selection signatures at autosomal loci interacting with mitochondria, providing insights into the hybridization of mammalian species.
Article
Plant Sciences
Heitor Calux Mendonca, Luiz Filipe Protasio Pereira, Joao Vitor Maldonado dos Santos, Anderson Rotter Meda, Gustavo Cesar Sant' Ana
Summary: This study analyzed the population structure and genetic diversity of Brazilian soybean and found a narrow genetic base. The results showed that the region of origin, company of origin, and relative maturity group significantly influenced population structure. Brazilian soybean had lower genetic diversity compared to Asian accessions. Furthermore, the study identified genomic regions under selection that may be associated with soybean adaptation to Brazilian environments.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Evolutionary Biology
Turid Everitt, Andreas Wallberg, Matthew J. Christmas, Anna Olsson, Wolfgang Hoffmann, Peter Neumann, Matthew T. Webster
Summary: Different genetic architectures underlie local adaptation in nature. Eastern African honey bees harbor two chromosomal inversions that likely govern adaptation to high-elevation habitats. In the Americas, honey bees are hybrids of European and African ancestries and adaptation to climate variation correlates with the proportion of these ancestries. The study sequenced the genomes of honey bees from high- and low-elevation populations in Colombia and found that highland bees had a higher proportion of European ancestry and exhibited genetic differentiation related to reproduction and sperm competition. Variation in European ancestry levels was correlated between highland honey bees and populations at higher latitudes in South America, suggesting adaptation to both latitude and elevation mediated by ancestry across the genome.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Agriculture, Dairy & Animal Science
F. J. M. King, C. Visser, C. Banga
Summary: Knowledge of genetic variability among cattle populations is essential to gain insight into the adaptation mechanisms and to support the conservation of genetic resources. This study investigated the levels of genetic diversity and relationships between indigenous cattle breeds using genotyping techniques. The results showed that there was little genetic distance between Nguni populations, while Tuli and Boran populations were more divergent. Additionally, several genes related to adaptation and production traits were identified.
Article
Immunology
Fernando Flores Cardoso, Oswald Matika, Appolinaire Djikeng, Ntanganedzeni Mapholi, Heather M. Burrow, Marcos Jun Iti Yokoo, Gabriel Soares Campos, Claudia Cristina Gulias-Gomes, Valentina Riggio, Ricardo Pong-Wong, Bailey Engle, Laercio Porto-Neto, Azwihangwisi Maiwashe, Ben J. Hayes
Summary: This study evaluated tick resistance in multiple beef cattle breeds, revealing differences in genetic correlations and heritability among populations, as well as the potential benefits of multi-trait genomic selection. The multi-trait approach improved predictive ability and corrected over-dispersion of GEBV, showing promise for enhancing tick resistance in beef cattle through genomic selection.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Paulo Alvarez Cecco, Andres Rogberg Munoz, Marianela Balbi, Martin Bonamy, Sebastian Munilla, Natalia Soledad Forneris, Pilar Peral Garcia, Rodolfo Juan Carlos Cantet, Guillermo Giovambattista, Maria Elena Fernandez
Summary: This study estimated the breed composition of the Argentinean Brangus population and identified genomic regions with positive selection signatures. The findings contribute to the understanding of the genetic mechanisms involved in cross-bred cattle adaptation and productivity in tropical environments.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Wondossen Ayalew, Xiaoyun Wu, Getinet Mekuriaw Tarekegn, Tesfaye Sisay Tessema, Rakan Naboulsi, Renaud Van Damme, Erik Bongcam-Rudloff, Zewdu Edea, Solomon Enquahone, Ping Yan
Summary: This study presents the first whole-genome sequencing of Abigar cattle, revealing genes associated with heat tolerance, immune response, and stress resilience in tropical conditions. These findings are of great importance for understanding and improving the adaptive traits of Abigar cattle.
Article
Biochemistry & Molecular Biology
Maria Bogaerts-Marquez, Sara Guirao-Rico, Mathieu Gautier, Josefa Gonzalez
Summary: This study analyzed 36 whole-genome pool-seq samples of D. melanogaster natural populations collected in 20 European and 11 North American locations, and identified temperature, rainfall, and wind related variables as relevant for D. melanogaster environmental adaptation. The analysis also found SNPs and transposable elements associated with environmental variables.
Article
Genetics & Heredity
Bruno Serranito, Dominique Taurisson-Mouret, Sahraoui Harkat, Abbas Laoun, Nadjet-Amina Ouchene-Khelifi, Francois Pompanon, Badr Benjelloun, Giuliano Cecchi, Sophie Thevenon, Johannes A. Lenstra, Anne Da Silva
Summary: This study analyzed two datasets of goats from West-Central Africa and East Africa using LFMM and PCAdapt to identify molecular signatures related to trypanotolerance. The most plausible signatures of trypanotolerance point to specific genes. The study highlights the importance of protecting local breeds.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Mathieu Gautier, Renaud Vitalis, Laurence Flori, Arnaud Estoup
Summary: By capturing the structuring of genetic variation across populations, F-statistics have proven effective in inferring demographic history. A reinterpretation of F (and D) parameters has led to unbiased estimators for Pool-Seq data and standard allele count data. The new package poolfstat provides a user-friendly and efficient tool for unraveling complex population genetic histories.
MOLECULAR ECOLOGY RESOURCES
(2022)
Review
Parasitology
Marc Desquesnes, Marisa Gonzatti, Alireza Sazmand, Sophie Thevenon, Geraldine Bossard, Alain Boulange, Geoffrey Gimonneau, Philippe Truc, Stephane Herder, Sophie Ravel, Denis Sereno, Vincent Jamonneau, Sathaporn Jittapalapong, Philippe Jacquiet, Philippe Solano, David Berthier
Summary: This review discusses the reliable and up-to-date methods for diagnosing trypanosomoses caused by trypanosomes in wild and domestic mammals. The diseases have significant impact on human and animal health, as well as livestock economy. The review covers various diagnostic methods including parasite detection, DNA detection, and antibody detection, while considering factors such as sensitivity, specificity, and cost constraints. It also addresses the challenge of diagnosing mixed infections and the importance of improving diagnostic procedures worldwide for better infection control and One Health.
PARASITES & VECTORS
(2022)
Article
Multidisciplinary Sciences
Alexander Klassmann, Mathieu Gautier
Summary: Analysis of population genetic data often involves the search for genomic regions with signs of recent positive selection. In this study, we propose and test modifications to the concept of extended haplotype homozygosity (EHH) and its associated statistics to relax data requirements. Our findings show the indispensability of phased haplotypes for accurate estimation of within-population statistics and cross-population statistics for small samples. Ancestry information, however, is found to be less important for both types of statistics. Our modified statistics are implemented in the publicly available R package rehh.
Article
Parasitology
G. Bossard, L. Millogo, S. Thevenon, H. Vitouley, Z. Bengaly, M. Desquesnes
Summary: By evaluating and validating the use of dehydrated reagents and serum samples, a convenient approach was provided for improving the serological diagnosis of animal trypanosomoses due to trypanosomes of African origin. This improvement may extend to regional laboratories, supporting disease control and research efforts in endemic countries.
VETERINARY PARASITOLOGY
(2021)
Article
Genetics & Heredity
Jessica Magnier, Tom Druet, Michel Naves, Melissa Ouvrard, Solene Raoul, Jerome Janelle, Katayoun Moazami-Goudarzi, Matthieu Lesnoff, Emmanuel Tillard, Mathieu Gautier, Laurence Flori
Summary: Despite their central economic and cultural role, the origin of cattle populations living in Indian Ocean islands remains poorly documented. In this study, using high-density SNP genotyping data, the researchers unraveled the demographic and adaptive histories of the Zebus from Mayotte and Madagascar. They found that these populations are closely related and have a predominant indicine ancestry. The divergence between these populations occurred in the 16th century with the arrival of European people and the transformation of the trade network in the area. The common ancestral cattle population originated from an admixture between an African zebu population and an Indian zebu around the 12th century during the earliest contacts between human African populations and Austronesian people in Comoros and Madagascar. The study also identified candidate genes involved in various biological functions related to physiological adaptation to tropical conditions.
G3-GENES GENOMES GENETICS
(2022)
Article
Infectious Diseases
Magamba Tounkara, Alain Boulange, Magali Thonnus, Frederic Bringaud, Adrien Marie Gaston Belem, Zakaria Bengaly, Sophie Thevenon, David Berthier, Loic Riviere
Summary: African animal trypanosomiasis (AAT) is a prevalent disease in sub-Saharan Africa, hindering livestock production development. This study evaluated the diagnostic potential of TbLysoPLA and TbGK proteins from Trypanosoma brucei in indirect ELISA for antibody detection. The results showed that the combination of these proteins with the BiP protein of T. congolense improved sensitivity and specificity compared to individual testing, demonstrating the importance of protein combinations in the diagnosis of AAT.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Ecology
Tom Druet, Mathieu Gautier
Summary: Inbreeding refers to mating of related individuals, which brings together harmful genetic variations in one individual. Genomic estimations of inbreeding coefficients are more preferred than pedigree-based estimators due to their ability to measure actual inbreeding levels and their robustness against pedigree errors. Recent developments in hidden Markov models (HMM) have provided valuable methods for identifying homozygous-by-descent (HBD) segments, particularly in cases of degraded or heterogeneous data. This study proposes a new model that classifies HBD segments into nested levels based on expected segment lengths, with improved statistical properties and performance compared to previous versions. The new model allows for a better partitioning of inbreeding in different HBD classes.
THEORETICAL POPULATION BIOLOGY
(2022)
Review
Parasitology
Marc Desquesnes, Alireza Sazmand, Marisa Gonzatti, Alain Boulange, Geraldine Bossard, Sophie Thevenon, Geoffrey Gimonneau, Philippe Truc, Stephane Herder, Sophie Ravel, Denis Sereno, Etienne Waleckx, Vincent Jamonneau, Philippe Jacquiet, Sathaporn Jittapalapong, David Berthier, Philippe Solano, Laurent Hebert
Summary: Reliable diagnostic tools are necessary to effectively treat and control animal trypanosomoses, which can be pathogenic. This review emphasizes the implementation of previously reviewed diagnostic methods in complex scenarios, and highlights the need for an integrative approach that combines parasite detection, DNA/RNA/antigen detection, antibody detection, and epizootiological information. While antibody detection tests have high sensitivity, DNA-based methods are more specific. Further developments are required to address gaps in current diagnostic methods and to improve prevention and control of animal trypanosomoses.
PARASITES & VECTORS
(2022)
Article
Agriculture, Dairy & Animal Science
Ayao Missohou, Basse Kabore, Laurence Flori, Simplice Bosco Ayssiwede, Jean-Luc Hornick, Marianne Raes, Jean-Francois Cabaraux
Summary: This study reported the genetic parameters of four Senegalese sheep breeds and their relationship with global sheep breeds. The results provided insights into genetic conservation and adaptability of these breeds in the Senegalese context. The study also revealed the contribution of Senegalese sheep breeds to global genetic diversity and the development of Caribbean sheep breeds.
Article
Parasitology
Kadidiata Ilboudo, Robert Eustache Hounyeme, Jacques Kabore, Alain Boulange, Geoffrey Gimonneau, Ernest Salou, Adrien Gaston Marie Belem, Veerle Lejon, Charlie Franck Alfred Compaore, Bruno Bucheton, Mathurin Koffi, Philippe Solano, David Berthier, Sophie Thevenon, Vincent Jamonneau
Summary: Reliable diagnostic tools are crucial in the elimination process of human African trypanosomiasis. The immune trypanolysis test (TL) using variant antigen types (VAT) LiTat 1.3 and LiTat 1.5 is a promising tool, but its specificity has been questioned. This study evaluates the performance of TL in pigs experimentally infected with Trypanosoma brucei brucei.
Article
Evolutionary Biology
Laure Olazcuaga, Julien Foucaud, Candice Deschamps, Anne Loiseau, Jean-Loup Claret, Romain Vedovato, Robin Guilhot, Cyril Sevely, Mathieu Gautier, Ruth A. Hufbauer, Nicolas O. Rode, Arnaud Estoup
Summary: The study demonstrates that local adaptation can rapidly evolve in natural populations even under spatially and temporally variable selection conditions, with genetic effects dominating over plastic effects.