Article
Entomology
Jinyu Li, Longqing Shi, Wei Chen, Yi Mao, Liette Vasseur, Geoff Gurr, Minsheng You, Shijun You
Summary: The study on the tea green leafhopper found that climatic differences play a significant role in the subpopulation differentiation of the leafhopper, which explains the observed increase in outbreak frequency under climate change. This study also demonstrates the usefulness of molecular genetic approaches in studying the effects of environmental heterogeneity on natural population genetic variation.
ENTOMOLOGIA GENERALIS
(2023)
Review
Endocrinology & Metabolism
Sean Bankier, Tom Michoel
Summary: Hormonal variations affect phenotypic responses by altering gene expression. Genetic variants related to hormones can be analyzed through gene expression changes, and eQTLs can be used as causal inference tools. Hormone networks driven by transcription factors are associated with eQTLs.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Multidisciplinary Sciences
Thibault Latrille, Nicolas Rodrigue, Nicolas Lartillot
Summary: Adaptation in protein-coding sequences can be detected using either multiple sequence alignments across species or polymorphism data within a population. Traditional phylogenetic codon models have limitations due to purifying selection, but recent developments in mutation-selection codon models provide a more detailed assessment of mutation, purifying, and positive selection. This exome-wide analysis shows that proteins and sites detected to be under adaptation at the phylogenetic scale are also under adaptation at the population-genetic scale, reconciling the two approaches and enabling integrative models and analyses across individuals and populations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Ecology
Marty Kardos, Gordon Luikart
Summary: The genetic architecture underlying heritability significantly impacts population viability during environmental change, with polygenic trait architectures showing higher viability compared to architectures with large-effect loci. Initial frequency of large-effect beneficial alleles also plays a crucial role in population viability, with moderately low initial allele frequencies conferring higher viability. Integrating information on trait genetic architecture into analysis will improve understanding and prediction of evolutionary and demographic responses to environmental change.
AMERICAN NATURALIST
(2021)
Article
Biochemistry & Molecular Biology
Natalie R. Hofmeister, Scott J. Werner, Irby J. Lovette
Summary: Genomic research on North American starlings indicates low geographical differentiation and few significant F-ST outliers at a continental scale, despite their high dispersal rate and rapid expansion history. Despite starting from a relatively small founding population, these birds show only moderate genetic bottleneck and a dramatic increase in effective population size since introduction. Furthermore, single-nucleotide polymorphisms correlated with temperature and/or precipitation suggest rapid local adaptation in North American starlings even in their wide-ranging and evolutionarily young system.
Article
Evolutionary Biology
Marc A. Beer, Rachael A. Kane, Steven J. Micheletti, Christopher P. Kozakiewicz, Andrew Storfer
Summary: Understanding the genetic differentiation and local adaptation is crucial for addressing rapid environmental changes. This study investigates the genetic patterns and adaptation of the streamside salamander across its geographic range, providing insights into its potential response to environmental changes. The findings suggest a polygenic architecture of adaptation and identify candidate genes contributing to local adaptation.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Alejandro Llanos-Garrido, Andrea Briega-Alvarez, Javier Perez-Tris, Jose A. Diaz
Summary: By studying the correlation between genotypes of lizards and environmental factors, the research explored the impact of genetic variation on species distribution range. The results showed that genetic variation can affect species adaptability and distribution range. The experiment supports the relationship between genetic variation and species adaptability and environmental variation.
Article
Ecology
Yang Yu, Alan O. Bergland
Summary: Populations of short-lived organisms can adapt to spatial and temporal environmental heterogeneity through local adaptation, which can be reflected on both phenotypic and genetic levels. This study examines the patterns of allele frequency change at expression quantitative trait loci (eQTLs) across a latitudinal cline and between seasons, and finds that eQTLs are enriched for clinally varying polymorphisms. The study also suggests that clinal adaptation at eQTLs is at least partially distinct from seasonal adaptation.
Article
Biochemistry & Molecular Biology
Camille Kessler, Alice Brambilla, Dominique Waldvogel, Glauco Camenisch, Iris Biebach, Deborah M. Leigh, Christine Grossen, Daniel Croll
Summary: The study explores the impact of immune function polymorphism on health and reproductive success within species, as well as the significance of genetic diversity loss in extinction risk. Through the design of a microfluidics-based amplicon sequencing assay, comprehensive genetic variation in Alpine ibex was successfully captured, revealing unexpectedly high genetic differentiation at immunity-related loci within the species.
MOLECULAR ECOLOGY RESOURCES
(2022)
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
Multidisciplinary Sciences
R. Gacesa, A. Kurilshikov, A. Vich Vila, T. Sinha, M. A. Y. Klaassen, L. A. Bolte, S. Andreu-Sanchez, L. Chen, V. Collij, S. Hu, J. A. M. Dekens, V. C. Lenters, J. R. Bjork, J. C. Swarte, M. A. Swertz, B. H. Jansen, J. Gelderloos-Arends, S. Jankipersadsing, M. Hofker, R. C. H. Vermeulen, S. Sanna, H. J. M. Harmsen, C. Wijmenga, J. Fu, A. Zhernakova, R. K. Weersma
Summary: This study analyzed the gut microbiome of 8,208 individuals from the Netherlands and found that the microbiome is primarily shaped by the environment and cohabitation. Only about 6.6% of microbial taxa are heritable, while around 48.6% of taxa are significantly influenced by cohabitation. Additionally, the study identified numerous associations between the microbiome and health, diet, socioeconomic factors, and early-life and current exposome.
Article
Biochemistry & Molecular Biology
Soraia Barbosa, Kimberly R. Andrews, Amanda R. Goldberg, Digpal S. Gour, Paul A. Hohenlohe, Courtney J. Conway, Lisette P. Waits
Summary: This study examines the neutral and adaptive processes in species and population differentiation using recently diverged sister species of ground squirrels. The results highlight the importance of neutral and adaptive differentiation in understanding genetic structure and environmental adaptation, with implications for conservation efforts.
Article
Multidisciplinary Sciences
Kara J. Andres, David M. Lodge, Jose Andres
Summary: Environmental DNA (eDNA) sampling is a powerful and efficient approach for collecting information about species, and it may also provide information about population-level genetic variability. In this study, the researchers used eDNA sampling to estimate the genetic diversity and structure of an invasive fish species in the Great Lakes region. The study found that the genetic patterns observed from eDNA analysis were consistent with conventional tissue-based estimates. This research highlights the potential for eDNA sampling to reveal detailed population characteristics that can inform monitoring and management plans for difficult-to-sample species.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Evolutionary Biology
John K. Kelly
Summary: This study characterizes the evolution of SNPs in a population of yellow monkeyflower. It finds that most SNPs exhibit minimal change over time, consistent with neutral evolution. However, a subset of SNPs display strong fluctuations in frequency, which are driven by selection and have a ripple effect on genome-wide variation.
Article
Biotechnology & Applied Microbiology
Matt J. Thorstensen, Melinda R. Baerwald, Ken M. Jeffries
Summary: The study compared mRNA and microsatellite data sets of two populations of a minnow species in the San Francisco Estuary, finding that mRNA sequencing revealed patterns of population structure similar to microsatellites but with lower genetic variation. Phenotypic plasticity and signatures of selection were mostly mutually exclusive within individual genes.
Editorial Material
Medicine, Research & Experimental
Maureen R. Hanson, Zhenglong Gu, Alon Keinan, Kaixiong Ye, Arnaud Germain, Paul Billing-Ross
JOURNAL OF TRANSLATIONAL MEDICINE
(2016)
Article
Medicine, Research & Experimental
Paul Billing-Ross, Arnaud Germain, Kaixiong Ye, Alon Keinan, Zhenglong Gu, Maureen R. Hanson
JOURNAL OF TRANSLATIONAL MEDICINE
(2016)
Article
Ecology
Kaixiong Ye, Feng Gao, David Wang, Ofer Bar-Yosef, Alon Keinan
NATURE ECOLOGY & EVOLUTION
(2017)
Article
Geriatrics & Gerontology
Yuan Si, Xi Liu, Kaixiong Ye, Alessandro Bonfini, Xun Yang Hu, Nicolas Buchon, Zhenglong Gu
JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES
(2019)
Article
Immunology
Lu Huang, Kaixiong Ye, Michael C. McGee, Natalie F. Nidetz, Jessica P. Elmore, Candice B. Limper, Teresa L. Southard, David G. Russell, Avery August, Weishan Huang
FRONTIERS IN IMMUNOLOGY
(2020)
Article
Nutrition & Dietetics
Jingqi Zhou, Chang Liu, Michael Francis, Yitang Sun, Moon-Suhn Ryu, Arthur Grider, Kaixiong Ye
Article
Geriatrics & Gerontology
Jingqi Zhou, Yitang Sun, Weishan Huang, Kaixiong Ye
Summary: The genetic locus 3p21.31 may be associated with altered blood cell traits such as monocyte, eosinophil, and neutrophil, highlighting potential mechanistic links to severe COVID-19. Additionally, significant differences in white blood cell traits across age and sex groups were observed in the study, suggesting potential factors related to increased risk of severe COVID-19 in older adults and men.
JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES
(2021)
Article
Orthopedics
J. Zhou, C. Liu, Y. Sun, M. Francis, M. S. Ryu, A. Grider, K. Ye
Summary: Genetically determined copper and zinc status were positively associated with osteoarthritis, particularly increasing the risk of localized OA, while an increase in calcium levels decreased the risk of localized OA.
OSTEOARTHRITIS AND CARTILAGE
(2021)
Article
Health Care Sciences & Services
Yitang Sun, Jingqi Zhou, Kaixiong Ye
Summary: The study reveals causal protective effects of higher basophil count, basophil percentage of white blood cells, and myeloid white blood cell count on severe COVID-19, but no association with COVID-19 severity or susceptibility was found. Individuals with a lower genetic capacity for basophils may be at risk, while enhancing basophil production could be an effective therapeutic strategy.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Genetics & Heredity
Michael Francis, Changwei Li, Yitang Sun, Jingqi Zhou, Xiang Li, J. Thomas Brenna, Kaixiong Ye
Summary: Fish oil supplementation has mixed effects on circulating cardiovascular biomarkers, with genetic polymorphisms playing a role in the response of blood lipids to supplementation. This study identified four genetic loci where fish oil supplementation can modify the effects on blood lipids, highlighting the potential for personalized nutrition interventions to reduce cardiovascular disease risk.
Article
Multidisciplinary Sciences
Yiqin Wang, Xiaoxian Guo, Kaixiong Ye, Michael Orth, Zhenglong Gu
Summary: Mitochondrial dysfunction is accelerated in patients with Huntington's disease due to the presence of pathogenic mtDNA heteroplasmies, particularly in lymphoblasts. The expansion of these heteroplasmies is correlated with disease progression and severity, as well as decline in functional capacity. Additionally, elongated CAG repeats in the HTT gene contribute to the age-dependent expansion of pathogenic mtDNA heteroplasmies in HD patients.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Immunology
Qing Kong, Shiyu Xia, Xingxin Pan, Kaixiong Ye, Zhouyihan Li, Haoyan Li, Xiaoqiang Tang, Nidhi Sahni, S. Stephen Yi, Xing Liu, Hao Wu, Michael B. Elowitz, Judy Lieberman, Zhibin Zhang
Summary: Granzyme A enzyme from killer lymphocytes can cleave gasdermin B (GSDMB) and induce pyroptosis in targeted human tumor cells, leading to antitumor immunity. However, GSDMB has both anti- and pro-tumor functions. This study found that there are functionally distinct splicing variants of GSDMB, and only isoforms 3 and 4 can cause pyroptosis while isoforms 1, 2, and 5 cannot. Expression of cytotoxic GSDMB3/4 isoforms is associated with better outcomes in bladder and cervical cancers, suggesting their protective role in these tumors.
SCIENCE IMMUNOLOGY
(2023)
Editorial Material
Critical Care Medicine
Yitang Sun, Kaixiong Ye
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2023)
Article
Medicine, Research & Experimental
Yitang Sun, Jingqi Zhou, Kaixiong Ye
Summary: The study identified body mass index-related traits, specific white blood cells, and certain circulating proteins as potential risk factors for the development of severe COVID-19.
COMMUNICATIONS MEDICINE
(2021)
Article
Biotechnology & Applied Microbiology
Ruoyu Zhang, Yiqin Wang, Kaixiong Ye, Martin Picard, Zhenglong Gu