Article
Multidisciplinary Sciences
Moshe Shay Ben-Haim, Olga Dal Monte, Nicholas A. Fagan, Yarrow Dunham, Ran R. Hassin, Steve W. C. Chang, Laurie R. Santos
Summary: Scholars have debated the consciousness of animals for a long time, and research has identified two distinct processing modes in humans and monkeys. Through an empirical approach, it is possible to distinguish conscious visual awareness from nonconscious processing in nonhuman species.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Dan Qi Priscilla Oh, Iris Grothe, Herbert Lukass, Andreas K. Kreiter, Markus Hoffmann, Detlef Wegener
Summary: The availability of effective vaccines and high vaccination rates have allowed for the relaxation or removal of many protective measures for controlling the SARS CoV-2 pandemic. However, the emergence of new and highly mutated variants with increased transmissibility and reduced vaccine efficacy has led to high infection rates in the third year of the pandemic. The combination of reduced measures and increased infectivity poses a particular risk for unvaccinated individuals, including susceptible animals.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Elizabeth Wood, Zachary Baron, Ryno Kruger, Colt Halter, Natalia Gabrielle, Leslie Neville, Ellie Smith, Leah P. Marett, Miranda Johnson, Laura Del Rosso, John Capitanio, J. Dee Higley
Summary: Studies have shown that maternal behaviors are influenced by the bivariate serotonin transporter genotype (5-HTT), but there are mixed findings regarding the specific effects of the s allele. Nonhuman primate studies provide more control over extraneous variables and can help understand the impact of 5-HTT genotype on maternal sensitivity. This study examined 125 rhesus macaque mothers and found that those with the s allele demonstrated more neglectfulness and less restraint, indicating lower maternal sensitivity during the first three months of their infants' lives. These findings highlight the importance of considering maternal 5-HTT genotype in studies on maternal sensitivity and mother-infant attachment quality.
Review
Plant Sciences
Muhammad Yasir, Hafiza Hamrah Kanwal, Quaid Hussain, Muhammad Waheed Riaz, Muhammad Sajjad, Junkang Rong, Yurong Jiang
Summary: Over the past two decades, high-density SNP arrays and DNA sequencing technology have been widely used in crop research, particularly in cotton crops. Genome-wide association studies (GWAS) have provided an important tool for uncovering the relationship between crop phenotypes and underlying genetics, helping to advance crop breeding and improvement.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Dat Thanh Nguyen, Quan Hoang Nguyen, Nguyen Thuy Duong, Nam S. Vo
Summary: Despite the advancement of sequencing technology, SNP arrays remain the most cost-effective genotyping solution for large-scale genomic research. This study introduces a novel method called LmTag for tag SNP selection, which improves imputation performance and prioritizes highly functional SNP markers. It is particularly suitable for under-represented populations and non-model species in developing countries.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Evolutionary Biology
Jeffrey D. Wall, Jacqueline A. Robinson, Laura A. Cox
Summary: This study investigates crossover and noncrossover recombination in olive baboons and compares the results to linkage disequilibrium-based recombination estimates. The study finds gender differences in recombination rates and a bimodal distribution of noncrossover tract lengths. Additionally, the study demonstrates the use of crossover and linkage disequilibrium-based recombination estimates in identifying genome assembly errors.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Kate D. Lee, Craig D. Millar, Patricia Brekke, Annabel Whibley, John G. Ewen, Melanie Hingston, Amy Zhu, Anna W. Santure
Summary: Next-generation sequencing technology has revolutionized ecological and evolutionary genetics, enabling cost-effective identification of genome-wide variation. In this study, researchers developed a 50K SNP chip for the threatened species hihi by combining RAD-seq and WGS data, demonstrating its utility in identifying SNPs for genotyping and revealing high rates of linkage disequilibrium in the hihi genome, indicative of population bottleneck events.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Fisheries
Hao Wang, Jia Lv, Qifan Zeng, Yaran Liu, Qiang Xing, Shi Wang, Jingjie Hu, Lisui Bao
Summary: The bay scallop is an economically important bivalve species in aquaculture industry in China, with the highest annual yield. Through whole genomic resequencing analysis, researchers found that the selective breeds of bay scallop have lower levels of genomic polymorphism and increased linkage disequilibrium compared to the hatchery reference population. Selective sweep analysis revealed genes under selection in the two breeds, potentially contributing to improved growth and immunity performance.
Article
Ophthalmology
M. Isabel Casanova, Laura J. Young, Sangwan Park, Soohyun Kim, Karolina Roszak, Brian C. Leonard, Andrew Blandino, Monica J. Motta, Glenn Yiu, Jennifer Y. Li, Ala Moshiri, Sara M. Thomasy
Summary: The purpose of this study was to establish the normal range of central corneal thickness (CCT) and corneal endothelial cell density (ECD) in rhesus macaques and investigate the effects of age, body weight, sex, and intraocular pressure (IOP) on these parameters. The study found that the mean CCT values obtained by different measurement methods were significantly different, while the semiautomatic and manual ECD did not differ significantly. The CCT was associated with IOP and sex, while the ECD was associated with body weight and age. Corneal disease was also found to be uncommon in rhesus macaques.
TRANSLATIONAL VISION SCIENCE & TECHNOLOGY
(2022)
Article
Psychology, Biological
Anthony C. Santistevan, Gilda Moadab, Olivia Fiske, Christina M. Nord, Derek M. Isaacowitz, Eliza Bliss-Moreau
Summary: Aging has various effects on autonomic nervous system function, including differences in response to psychosocial stressors. Nonhuman primate models, such as aged rhesus monkeys, provide valuable insights into the sources of age-related differences.
Article
Fisheries
Baltasar F. Garcia, Alvaro Bonaguro, Carolina Araya, Roberto Carvalheiro, Jose M. Yanez
Summary: The inclusion of genomic information has accelerated genetic gain in shrimp breeding. Evaluating LD decay is crucial for assessing the feasibility of genomic selection. A study using a 50K SNP array tool characterized genomic diversity and LD in a farmed shrimp population.
AQUACULTURE REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
Pablo Federico Roncallo, Adelina Olga Larsen, Ana Laura Achilli, Carolina Saint Pierre, Cristian Andres Gallo, Susanne Dreisigacker, Viviana Echenique
Summary: This study evaluated the genetic diversity, population structure and linkage disequilibrium patterns in a durum wheat collection consisting of 197 genotypes using a 35K SNP array. The results showed a slight increase in genetic diversity over time, with a reduction in rare allelic variants after 1979. The level of pairwise loci in LD was low, and LD patterns varied across different breeding periods.
Article
Genetics & Heredity
Simone Rubinacci, Diogo M. Ribeiro, Robin J. Hofmeister, Olivier Delaneau
Summary: GLIMPSE is a new method for haplotype phasing and genotype imputation of low-coverage sequencing datasets, showing remarkable performance across different coverages and human populations. This method achieves genome imputation at a cost lower than US$1, outperforming other methods and improving imputation accuracy over the full allele frequency range. The study indicates the promising potential of low-coverage imputation and suggests a paradigm shift in the design of future genomic studies.
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
Environmental Sciences
Hao Wang, Mingxuan Teng, Pingping Liu, Mingyang Zhao, Shi Wang, Jingjie Hu, Zhenmin Bao, Qifan Zeng
Summary: The study on Pacific white shrimps through whole genomic resequencing has revealed the genetic effects of artificial selection and genetic differentiation among different breeds, providing valuable information for germplasm resources assessment and genome-assisted breeding of Pacific white shrimps.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Anthropology
Jelmer W. Eerkens, Traci Carlson, Ripan S. Malhi, Jennifer Blake, Eric J. Bartelink, Gry H. Barfod, Alan Estes, Ramona Garibay, Justin Glessner, Alexandra M. Greenwald, Kari Lentz, Hongjie Li, Charla K. Marshall
AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY
(2016)
Article
Anthropology
Elizabeth K. Mallott, Paul A. Garber, Ripan S. Malhi
AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY
(2017)
Article
Veterinary Sciences
Xinjun Zhang, Yuhuan Meng, Paul Houghton, Mingyu Liu, Sreetharan Kanthaswamy, Robert Oldt, Jillian Ng, Jessica Satkoski Trask, Ren Huang, Balbir Singh, Hongli Du, David Glenn Smith
JOURNAL OF MEDICAL PRIMATOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Lu Yao, Hongjie Li, Robert D. Martin, Corrie S. Moreau, Ripan S. Malhi
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2017)
Article
Multidisciplinary Sciences
John Lindo, Alessandro Achilli, Ugo A. Perego, David Archer, Cristina Valdiosera, Barbara Petzelt, Joycelynn Mitchell, Rosita Worl, E. James Dixon, Terence E. Fifield, Morten Rasmussen, Eske Willerslev, Jerome S. Cybulski, Brian M. Kemp, Michael DeGiorgio, Ripan S. Malhi
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2017)
Article
Genetics & Heredity
J. Eldon Molto, Odile Loreille, Elizabeth K. Mallott, Ripan S. Malhi, Spence Fast, Jennifer Daniels-Higginbotham, Charla Marshall, Ryan Parr
Article
Anthropology
Elizabeth K. Mallott, Katherine R. Amato, Paul A. Garber, Ripan S. Malhi
AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY
(2018)
Article
Genetics & Heredity
Alida de Flamingh, Ashley Coutu, Alfred L. Roca, Ripan S. Malhi
G3-GENES GENOMES GENETICS
(2020)
Article
Biochemistry & Molecular Biology
Alida de Flamingh, Ashley Coutu, Judith Sealy, Shadreck Chirikure, Armanda D. S. Bastos, Nzila M. Libanda-Mubusisi, Ripan S. Malhi, Alfred L. Roca
Summary: The oldest known shipwreck in southern Africa, discovered in Namibia in 2008, has revealed that the ivory cargo, including over 100 elephant tusks, came from African forest elephants in West Africa, providing insights into historic trade routes and the distribution of elephant populations in the region.
Article
Multidisciplinary Sciences
Angela R. Perri, Tatiana R. Feuerborn, Laurent A. F. Frantz, Greger Larson, Ripan S. Malhi, David J. Meltzer, Kelsey E. Witt
Summary: Advances in ancient DNA analysis have revealed close relationships between human and dog population histories, suggesting that dogs were domesticated in Siberia around 23,000 years ago and accompanied humans as they rapidly dispersed into the Americas around 15,000 years ago.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Evolutionary Biology
Alida de Flamingh, Angel G. Rivera-Colon, Tom P. Gnoske, Julian C. Kerbis Peterhans, Julian Catchen, Ripan S. Malhi, Alfred L. Roca
Summary: Numt Parser program identifies DNA sequences from numt pseudogene DNA, by comparing sequencing reads against cymt and numt reference sequences. It classifies reads into cymt or numt datasets, reducing sequence disagreements and equalizing read coverage across the mitogenome. Compared to other bioinformatic approaches, Numt Parser outperforms in identifying numt sequences while having minimal impacts on the recovery of cymt reads. It improves the reconstruction of true mitogenomes, allowing for accurate and robust biological inferences.
JOURNAL OF HEREDITY
(2023)
Article
Genetics & Heredity
Emma Kowal, Laura S. Weyrich, Juan Manuel Arguelles, Alyssa C. Bader, Chip Colwell, Amanda Daniela Cortez, Jenny L. Davis, Gonzalo Figueiro, Keolu Fox, Ripan S. Malhi, Elizabeth Matisoo-Smith, Ayushi Nayak, Elizabeth A. Nelson, George Nicholas, Maria A. Nieves-Colon, Lynette Russell, Sean Ulm, Francisco Vergara-Silva, Fernando A. Villanea, Jennifer K. Wagner, Joseph M. Yracheta, Krystal S. Tsosie
Summary: This article responds to the guidelines on the ethics of DNA research on human remains, arguing that they fail to consider the interests of community stakeholders. It highlights three main concerns with the guidelines, including the false separation of scientific and community concerns and the exclusion of community perspectives. The article stresses the importance of consulting communities with established or potential ties to Ancestors in research.
HUMAN GENETICS AND GENOMICS ADVANCES
(2023)
Review
Anthropology
Alyssa C. Bader, Aimee E. Carbaugh, Jenny L. Davis, Krystiana L. Krupa, Ripan S. Malhi
Summary: In the United States, the NAGPRA provides a framework for the disposition of Native American Ancestral remains, but biological samples taken from these remains have been treated independently and used in destructive research without consultation or consent from Native American communities. We argue that these samples should be handled according to regulations for human remains under NAGPRA, proposing best practices for their use and care specific to the United States context.
AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY
(2023)
Article
Veterinary Sciences
Xinjun Zhang, Sree Kanthaswamy, Jessica S. Trask, Jillian Ng, Robert F. Oldt, Joseph L. Mankowski, Robert J. Adams, David G. Smith
JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE
(2017)
Article
Genetics & Heredity
Caress Dean, Amanda J. Fogleman, Whitney E. Zahnd, Alexander E. Lipka, Ripan Singh Malhi, Kristin R. Delfino, Wiley D. Jenkins
JOURNAL OF COMMUNITY GENETICS
(2017)
Article
Biotechnology & Applied Microbiology
Zutan Li, Bingbing Jin, Jingya Fang
Summary: In this study, we propose MetaAc4C, an advanced deep learning model for accurate identification of N4-acetylcytidine (ac4C) sites using pre-trained BERT and various optimization techniques. By adapting generative adversarial networks to address data imbalance and augmenting training RNA samples, our model outperforms existing methods in terms of ACC, MCC, and AUROC.