Article
Plant Sciences
Chaoqiang Zhang, Yiwei Tang, Defeng Tian, Yanyan Huang, Guanghui Yang, Peng Nan, Yuguo Wang, Lingfeng Li, Zhiping Song, Ji Yang, Yang Zhong, Wenju Zhang
Summary: Population genetic structure plays a crucial role in conserving genetic resources and understanding evolution. However, its importance is often underestimated when using the most popular method and software for evaluation. This study found that hierarchical STRUCTURE analysis is more accurate in assessing genetic structure than traditional methods.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Kathryn H. Stankiewicz, Kate L. Vasquez Kuntz, Iliana B. Baums
Summary: The traditional method Delta K for determining population structure may underestimate the true number of clusters and be sensitive to uneven sampling. Using a combination of different estimators is recommended for more accurate results, as relying on a single estimator may not be sufficient in determining the optimal number of clusters.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Genetics & Heredity
Cuicui Wang, Bingbing Jiang, Junmin Liang, Leifu Li, Yilin Gu, Jintang Li, Yong Luo, Zhanhong Ma
Summary: The study revealed that there are distinct genotypic and genetic diversity levels among Pst subpopulations in Hubei province across different seasons and locations. Limited genotype exchange was observed between the populations of Gansu-Ningxia and Hubei provinces.
Article
Agronomy
Dongxue Yan, Liang Huang, Yun Xing, Hongfu Li, Chongjing Xia, Aolin Wang, Li Gao, Taiguo Liu, Wanquan Chen
Summary: Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), had a severe outbreak in the middle and lower reaches of the Yangtze River in 2019, while the disease was mild in north-western China. By analyzing the genetic structure of 210 Pst samples collected from the Yangtze River basin, it was found that the autumn inoculum sources of wheat stripe rust in 2019 in the middle and lower reaches of the Yangtze River probably originated from south-western over-summering areas through long-distance migration. Additionally, Jingzhou and adjacent areas in Hubei Province play an important role as a bridge or stopover for the inoculum sources.
Article
Plant Sciences
Subodh Adhikari, Samuel R. Revolinski, Sanford D. Eigenbrode, Ian C. Burke
Summary: The study investigated the genetic diversity and population structures of Mayweed chamomile from different invaded regions, identifying low but significant genetic variations among regions, populations, and individuals. Despite weak genetic structure, two main genetic clusters were identified, indicating potential gene flow among populations from different regions in the Pacific Northwest, USA.
Article
Biochemistry & Molecular Biology
Maike L. Morrison, Nicolas Alcala, Noah A. Rosenberg
Summary: In model-based inference of population structure, individuals are assigned membership coefficients in statistical clusters generated by clustering algorithms. Different groups of individuals can have distinct patterns of variability in their membership coefficients, which are difficult to capture using a single numerical value. We introduce a method that measures the variability of membership coefficients in a predefined group, using an analogy between individual membership coefficient vectors and population allele frequency vectors. Our approach makes use of a normalized F-ST statistic and can be used to compare and analyze inferred population structures.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Microbiology
Jian Ling, Xin Dong, Xingxing Ping, Yan Li, Yuhong Yang, Jianlong Zhao, Xiaofei Lu, Bingyan Xie, Zhenchuan Mao
Summary: This study investigated the genetic diversity and population structure of the cabbage fusarium wilt pathogen, FOC1, in northern China. The results showed that Chinese FOC1 can be grouped into four populations, and the genetic diversity is closely associated with geographical locations. The study also revealed genetic differentiation when FOC1 spread from Beijing to northwest provinces. This research provides insights into FOC1 variation and suggestions for cabbage fusarium wilt control in China.
Article
Genetics & Heredity
Katie Willis, Austin Burt
Summary: Synthetic gene drive systems offer efficient interventions for controlling disease vectors and pest species. It is possible to restrict the spread of gene drives by exploiting sequence differences between target and non-target populations. Double drive designs can be particularly effective for localized genetic control when there is genetic differentiation between populations.
Article
Marine & Freshwater Biology
Emily L. Boring, Bruce A. Menge, Felipe S. Barreto
Summary: Quantifying gene flow patterns is crucial in predicting the resilience of marine communities. Brooding species, which lack a pelagic larval phase, may be more susceptible to extinction. In this study, the population genetic structure of Leptasterias sp., a brooding sea star, was investigated. The results showed varying genetic structure at different spatial scales, suggesting that connectivity and genetic structure can be influenced by local and environmental factors, even in sessile brooding species.
Article
Genetics & Heredity
Alejandro Ochoa, John D. Storey
Summary: Kinship coefficients and F-ST are key parameters in modern population genetics studies, but existing estimators are biased due to restrictive assumptions when real datasets are considered. This study found that existing estimators can lead to severe biases and proposed a new estimation framework that is practically unbiased for any population structure. The new approach, demonstrated through theory and simulations, has the potential to significantly improve downstream analyses requiring accurate kinship and F-ST estimates.
Article
Entomology
Daniel Zamora-Mejias, Roberto-Emiliano Trejo-Salazar, Luis E. Eguiarte, Margarita Ojeda, Bernal Rodriguez-Herrera, Juan B. Morales-Malacara, Rodrigo A. Medellin
Summary: The genetic diversity and population genetic structure of the ectoparasite Periglischrus paracaligus were analyzed in association with the lesser long-nosed bat in Mexico, revealing diverse haplotype diversity and a historical demographic expansion process. No genetic structuring was observed in the parasite populations along with the distribution of the host species L. yerbabuenae in Mexico.
JOURNAL OF MEDICAL ENTOMOLOGY
(2022)
Article
Ecology
Simon Jacobsen Ellerstrand, Shruti Choudhury, Kajsa Svensson, Martin N. Andersson, Carsten Kirkeby, Daniel Powell, Fredrik Schlyter, Anna Maria Jonsson, Mikkel Brydegaard, Bengt Hansson, Anna Runemark
Summary: Research shows that the population structure of the Eurasian spruce bark beetle in Sweden is weak, indicating a high capacity for dispersion and establishment of outbreak populations in new territories.
ECOLOGY AND EVOLUTION
(2022)
Article
Chemistry, Multidisciplinary
Aijia Wei, Jinping Mu, Rui He, Xue Bai, Xiaohui Li, Lihui Zhang, Yanji Wang, Zhenfa Liu, Suning Wang
Summary: K+/Cl- and K+/F- co-doped LNMO materials were synthesized successfully, reducing impurities, enlarging lattice parameters, and improving cycling performance. Co-doping decreased particle size, enhanced Li+ diffusion, modified crystal structures, and increased electrochemical kinetics. The co-doped samples exhibited improved rate capability and cycling stability.
Article
Environmental Sciences
Rui Ding, Qiang Sun, Hailiang Jia, Shengze Xue, Qingmin Shi
Summary: The present study investigates the pore structure characteristics of coal samples from eleven coal mines in northern China and explores its relationship with the radon exhalation rate. It is found that low-rank coals have dominant micropores while medium and high-rank coals have dominant mesopores. The volume of mesopores and micropores in medium and high-rank coal samples is controlled by ash yield. The radon emission rate shows a positive linear correlation with the micropore volumes of the analyzed coal samples.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Multidisciplinary Sciences
Alexander T. Sentinella, Angela T. Moles, Jason G. Bragg, Maurizio Rossetto, William B. Sherwin
Summary: Accurately detecting sudden changes in genetic diversity is important for understanding gene flow barriers, identifying important loci, and defining management units. However, there is little information on the most robust metric for detecting these changes. This study aimed to determine the best measure for genetic step detection using SNP data. The results showed that alpha diversity based measures were ineffective, while beta diversity measures such as Shannon Information and Bray-Curtis dissimilarity were better at detecting steps. No single measure was best overall, and a combination of approaches is recommended for step detection.
Article
Microbiology
Thomas J. D. Coulson, Rene M. Malenfant, Cheryl L. Patten
Summary: Genome-wide RNA sequencing revealed a broader regulatory role for the TyrR transcription factor in the ecologically versatile bacterium Enterobacter ludwigii beyond that of aromatic amino acid synthesis and transport that constitute the role of the TyrR regulon of E. coli. In E. ludwigii, a plant symbiont and human gut commensal, the TyrR regulon is expanded to include genes that are beneficial for plant interactions and response to stresses. Identification of the genes regulated by TyrR provides insight into the mechanisms by which the bacterium adapts to its environment.
JOURNAL OF BACTERIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yin-Hong Cao, Song-Song Xu, Min Shen, Ze-Hui Chen, Lei Gao, Feng-Hua Lv, Xing-Long Xie, Xin-Hua Wang, Hua Yang, Chang-Bin Liu, Ping Zhou, Peng-Cheng Wan, Yun-Sheng Zhang, Jing-Quan Yang, Wen-Hui Pi, EEr Hehua, Donagh P. Berry, Mario Barbato, Ali Esmailizadeh, Maryam Nosrati, Hosein Salehian-Dehkordi, Mostafa Dehghani-Qanatqestani, Arsen Dotsev, Tatiana E. Deniskova, Natalia A. Zinovieva, Gottfried Brem, Ondrej Stepanek, Elena Ciani, Christina Weimann, Georg Erhardt, Joram M. Mwacharo, Abulgasim Ahbara, Jian-Lin Han, Olivier Hanotte, Joshua M. Miller, Zijian Sim, David Coltman, Juha Kantanen, Michael W. Bruford, Johannes A. Lenstra, James Kijas, Meng-Hua Li
Summary: The study found that genetic introgression from wild relatives enhanced climatic adaptation and resistance to pneumonia in domestic sheep populations. Specific alleles from genes like PADI2 were associated with resistance to pneumonia, contributing to the adaptation of sheep to varying climatic and environmental conditions after domestication.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Zoology
Evan W. Hessels, Eric C. Lofroth, Richard D. Weir, Jamieson C. Gorrell
Summary: Molecular analyses of genetic diversity in Vancouver Island wolverine population did not show significant genetic distinction from mainland population, suggesting that conservation efforts should focus on estimating population size and potential for natural recolonization.
JOURNAL OF MAMMALOGY
(2021)
Editorial Material
Ecology
Ivan Paz-Vinas, Evelyn L. Jensen, Laura D. Bertola, Martin F. Breed, Brian K. Hand, Margaret E. Hunter, Francine Kershaw, Deborah M. Leigh, Gordon Luikart, Joachim Mergeay, Joshua M. Miller, Charles B. Van Rees, Gernot Segelbacher, Sean Hoban
Summary: The study by Millette et al. did not find consistent anthropogenic effects on animal genetic diversity worldwide. However, reexamination of the data revealed limitations related to genetic markers and scale which may lead to misinterpretations with conservation implications. Suggestions were provided for improving future macrogenetic studies.
Review
Genetics & Heredity
Deborah M. Leigh, Charles B. van Rees, Katie L. Millette, Martin F. Breed, Chloe Schmidt, Laura D. Bertola, Brian K. Hand, Margaret E. Hunter, Evelyn L. Jensen, Francine Kershaw, Libby Liggins, Gordon Luikart, Stephanie Manel, Joachim Mergeay, Joshua M. Miller, Gernot Segelbacher, Sean Hoban, Ivan Paz-Vinas
Summary: Macrogenetics, a rapidly emerging field, focuses on analyzing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Despite its promising outlook, important limitations exist that need to be addressed for macrogenetics to reach its full potential.
NATURE REVIEWS GENETICS
(2021)
Article
Fisheries
Jessica R. Reilly, Joshua M. Miller
Summary: Arctic Grayling in Canada are divided into two deeply divergent lineages, with Alberta being a contact zone for the observed lineages. The divergence and geographic distribution of genetic diversity suggest that Arctic Grayling in Canada may merit consideration for separate designatable units.
NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT
(2021)
Article
Biodiversity Conservation
Joshua M. Miller, Erin O. Campbell, Jay J. Rotella, Kaitlin R. Macdonald, Thomas S. Gelatt, Corey S. Davis
Summary: Pedigrees have a long history in various fields such as classical genetics, agronomics, evolutionary ecology, and captive breeding, with the use of molecular techniques expanding the range of species for which pedigrees can be constructed. This study generated a novel set of genomic SNPs from ddRAD sequencing in two populations of Weddell seals, comparing parentage assignment rates and accuracy between different markers and software. The results showed higher parentage assignment rates using CERVUS compared to Sequoia, highlighting the importance of polarizing datasets for improved assignments.
CONSERVATION GENETICS RESOURCES
(2022)
Article
Biodiversity Conservation
Kimberley G. Barrett, Genevieve Amaral, Melanie Elphinstone, Malcolm L. McAdie, Corey S. Davis, Jasmine K. Janes, John Carnio, Axel Moehrenschlager, Jamieson C. Gorrell
Summary: Captive breeding is a last resort management option for conservation of endangered species, but can result in inbreeding depression and loss of genetic diversity. This study evaluated the success of the Vancouver Island marmot captive breeding program in preventing inbreeding and maintaining genetic diversity using high-throughput amplicon sequencing. The results showed that current studbooks are moderately effective at predicting genetic similarity, and captive and wild populations did not differ significantly in allelic frequencies, indicating successful conservation efforts in maintaining genetic diversity.
CONSERVATION GENETICS
(2022)
Article
Ecology
Joshua M. Miller, Dany Garant, Charles Perrier, Tristan Juette, Joel W. Jameson, Eric Normandeau, Louis Bernatchez, Denis Reale
Summary: The island syndrome hypothesis predicts that island populations should differ from mainland populations, with individuals on islands being larger, less aggressive, more sociable, and investing more in their offspring. Using genome-wide SNP markers, this study found clear genomic differentiation between island and mainland populations, with moderate to high marker-based heritability estimates for traits thought to underlie the ISH. Further analysis identified 12 loci associated with differentiation between mainland and island populations, suggesting independent evolutionary trajectories and a genetic basis for the traits considered.
Article
Ecology
Evelyn L. Jensen, Maud C. Quinzin, Joshua M. Miller, Michael A. Russello, Ryan C. Garrick, Danielle L. Edwards, Scott Glaberman, Ylenia Chiari, Nikos Poulakakis, Washington Tapia, James P. Gibbs, Adalgisa Caccone
Summary: The Galapagos Archipelago is a natural laboratory for studying evolution. Through genetic analysis of historical and contemporary giant tortoises from San Cristobal Island, researchers have discovered a distinct lineage and a closely related lineage. This finding underscores the value of museum samples and provides insights into the early evolution of these iconic turtles.
Article
Biology
Samuel Deakin, Marco Festa-Bianchet, Joshua M. Miller, Fanie Pelletier, David W. Coltman
Summary: In polygynous species, secondary sexual traits evolve through intrasexual competition for mates. This study challenges the assumption that underdeveloped sexual traits in one sex are a result of strong selection on the other sex. Female bighorn sheep with longer horns at 2 years of age have higher reproductive success and lifespan. There is a potential conservation issue as trophy hunting of males may decrease female reproductive performance and population growth.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Genevieve E. van der Voort, Scott R. Gilmore, Jamieson C. Gorrell, Jasmine K. Janes
Summary: Wild orchids, Platanthera dilatata and P. stricta, co-occur and overlap in flowering on Vancouver Island, Canada. Various insects interact with these orchids, but there are regional differences in floral visitors.
Editorial Material
Biochemistry & Molecular Biology
Catherine Cullingham, Rhiannon M. Peery, Joshua M. Miller
Summary: This article explores the internal mechanism of the discriminant analysis of principal components (DAPC) method, demonstrating the importance of parameter selection in model development and discussing the impact of over-fitting the model and how to evaluate DAPC model results. The author provides important guidelines to ensure researchers draw biologically relevant conclusions.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Forestry
Rhiannon M. Peery, Catherine Cullingham, David W. Coltman, Janice E. K. Cooke
Summary: This article reports a case study in which genomic tools were used to determine if lodgepole pine seedlings were sown from a contaminated seed source. With genotyping data, the researchers were able to determine the probable seed source of the suspect seedlings and make data-guided recommendations on their deployment. This case study demonstrates the importance of molecular markers in ensuring traceability in reforestation.
TREE GENETICS & GENOMES
(2022)