Article
Multidisciplinary Sciences
Wenwen Wang, Yujia Yang, Suxu Tan, Tao Zhou, Yang Liu, Changxu Tian, Lisui Bao, De Xing, Baofeng Su, Jinhai Wang, Yu Zhang, Shikai Liu, Huitong Shi, Dongya Gao, Rex Dunham, Zhanjiang Liu
Summary: The X and Y chromosomes of channel catfish have the same gene contents. The X-borne hydin-1 gene is silenced, while the Y-borne hydin-1 gene is expressed, resulting in monoallelic expression of hydin-1 responsible for sex determination, similar to genomic imprinting. Treatment with a methylation inhibitor, 5-aza-dC, erases the epigenetic marks and causes sex reversal.
Article
Multidisciplinary Sciences
Christophe Dufresnes, Alan Brelsford, Daniel L. Jeffries, Glib Mazepa, Tomasz Suchan, Daniele Canestrelli, Alfredo Nicieza, Luca Fumagalli, Sylvain Dubey, Inigo Martinez-Solano, Spartak N. Litvinchuk, Miguel Vences, Nicolas Perrin, Pierre-Andre Crochet
Summary: Research on frog and toad hybrid zones suggests that as lineages diverge, parts of the genome resist introgression, indicating that anuran speciation involves the gradual accumulation of multiple barrier loci scattered across the genome. This highly polygenic nature of reproductive isolation, along with the lack of hemizygous sex chromosomes, may explain the slower speciation clock in amphibians compared to other vertebrates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Christopher Keeling, Erin O. Campbell, Philip D. Batista, Victor A. Shegelski, Stephen A. L. Trevoy, Dezene P. W. Huber, Jasmine K. Janes, Felix A. H. Sperling
Summary: Advancements in genome sequencing methods and assembly tools have significantly improved the contiguity and gap reduction in insect genome assemblies since the draft genome assemblies of the mountain pine beetle were published in 2013. The new assemblies have greatly increased contiguity, with 90% of the content now contained in 12 and 11 scaffolds for the female and male assemblies, respectively. Analysis of two chromosome regions revealed significant differentiation between northern and southern Canadian populations.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Michail Rovatsos, Lukas Kratochvil
Summary: Organisms have evolved various mechanisms to cope with differences in gene copy numbers caused by degeneration of sex chromosomes. Different gene dose regulatory mechanisms were found in reptilian lineages with independently co-opted the same ancestral genomic region for sex chromosomes. The variability in gene dose regulation is not merely a consequence of ancestral autosomal gene content.
Article
Genetics & Heredity
Miao Ding, Xi-Yin Li, Zhi-Xuan Zhu, Jun-Hui Chen, Meng Lu, Qian Shi, Yang Wang, Zhi Li, Xin Zhao, Tao Wang, Wen-Xuan Du, Chun Miao, Tian-Zi Yao, Ming-Tao Wang, Xiao-Juan Zhang, Zhong-Wei Wang, Li Zhou, Jian-Fang Gui
Summary: Unisexual taxa are often considered short-lived due to the accumulation of deleterious mutations caused by the absence of meiotic recombination. However, the gynogenetic gibel carp has shown exceptional longevity and strong environmental adaptation. Male occurrence in this species is associated with male-specific microchromosomes containing homologous sequences of autosomes and abundant repetitive elements, which are likely the main driving force for male occurrence in gynogenetic gibel carp.
Article
Biotechnology & Applied Microbiology
Fan Jiang, Yaoxin Jiang, Wenxuan Wang, Changyi Xiao, Ruiyi Lin, Tanghui Xie, Wing-Kin Sung, Shijun Li, Ivan Jakovlic, Jianhai Chen, Xiaoyong Du
Summary: This study conducted chromosome-level genome assembly of the Muscovy duck and comparative genomic analysis, revealing unique gene families in Muscovy duck compared to other bird species, with adaptive evolution signals in immune defence pathways. The results provide valuable resources for future molecular ecology studies and the evolutionary arms race between hosts and influenza viruses.
Article
Biochemistry & Molecular Biology
Diana A. Robledo-Ruiz, Lana Austin, J. Nevil Amos, Jesus Castrejon-Figueroa, Daniel K. P. Harley, Michael J. L. Magrath, Paul Sunnucks, Alexandra Pavlova
Summary: Identifying sex-linked markers in genomic datasets is crucial for accurate genetic analysis and interpretation. However, current methods often neglect certain types of sex-linked variation. In this study, we developed new R functions that can reliably identify sex-linked loci and infer the genetic sex of individuals. We tested these functions on bird and mammal species and found that they achieved high accuracy in distinguishing sex-linked loci from autosomal loci. Furthermore, we demonstrated that failure to remove sex-linked loci can lead to incorrect biological inferences and management recommendations. Our functions provide a convenient tool for removing sex-linked loci in reduced-representation datasets and sexing individuals.
MOLECULAR ECOLOGY RESOURCES
(2023)
Editorial Material
Ecology
Yukiko M. Yamashita
Summary: A study manipulating heterochromatin content in Drosophila Y chromosomes found no association between Y chromosome length and longevity, challenging the hypothesis that Y chromosome-derived heterochromatin causes shorter lifespan in Y chromosome-bearing animals.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Genetics & Heredity
Carolina Crepaldi, Emiliano Marti, Evelin Mariani Goncalves, Dardo Andrea Marti, Patricia Pasquali Parise-Maltempi
Summary: Neotropical fishes have highly diversified karyotypic and genomic characteristics, with varied sex chromosome systems. The study on the satellitome of Megaleporinus elongatus revealed 140 different satDNA families, showing gender-biased differences and significant contributions to sex chromosome differentiation. The highly diversified satDNA composition in M. elongatus influences genome plasticity and evolutionary behavior in sex chromosomes.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Noelle Anderson, Kamil S. Jaron, Christina N. Hodson, Matthew B. Couger, Jan Sevcik, Brooke Weinstein, Stacy Pirro, Laura Ross, Scott William Roy
Summary: Haplodiploidy and paternal genome elimination are common in invertebrates and have evolved from male heterogamety. The importance of X chromosomes in this evolution is debated, with the Haploid Viability Hypothesis suggesting X-linked genes promote male haploidy, and the Intragenomic Conflict Hypothesis proposing conflict between genes as the driving force. By studying lineages with germline PGE and an XX/X0 system, we found increased X linkage in gPGE+X species, supporting the Intragenomic Conflict Hypothesis. These results provide evidence for the role of intragenomic conflict in the evolution of genetic systems like HD/PGE.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Nina Marchi, Laura Winkelbach, Ilektra Schulz, Maxime Brami, Zuzana Hofmanova, Jens Bloecher, Carlos S. Reyna-Blanco, Yoan Diekmann, Alexandre Thiery, Adamandia Kapopoulou, Vivian Link, Valerie Piuz, Susanne Kreutzer, Sylwia M. Figarska, Elissavet Ganiatsou, Albert Pukaj, Travis J. Struck, Ryan N. Gutenkunst, Necmi Karul, Fokke Gerritsen, Joachim Pechtl, Joris Peters, Andrea Zeeb-Lanz, Eva Lenneis, Maria Teschler-Nicola, Sevasti Triantaphyllou, Sofija Stefanovic, Christina Papageorgopoulou, Daniel Wegmann, Joachim Burger, Laurent Excoffier
Summary: Demogenomic modeling of ancient genomes sheds light on the genetic origins and differentiation process of early farming populations in Europe and Southwest Asia, as well as the genetic drift they experienced during their migration.
Review
Agriculture, Dairy & Animal Science
Marcello Mezzasalma, Elvira Brunelli, Gaetano Odierna, Fabio Maria Guarino
Summary: This article provides a comprehensive report on the presence of different types of polyploidy in tetrapods, with a particular focus on its genomic, evolutionary, and ecological diversity. It suggests that polyploidy is an important pathway of genomic evolution in tetrapods, occurring in most higher-taxa and displaying a variety of different forms, genomic configurations, and biological implications.
Article
Evolutionary Biology
Drew R. Schield, Blair W. Perry, Zachary L. Nikolakis, Stephen P. Mackessy, Todd A. Castoe
Summary: Male-biased mutation rates are found in a variety of organisms, especially those with ZW sex determination. A study on rattlesnakes found that male rattlesnakes have a 2.03-fold higher mutation rate compared to females, similar to findings in birds, suggesting that male-biased mutation rates may be a common feature in vertebrate lineages with ZW sex determination.
JOURNAL OF HEREDITY
(2021)
Article
Multidisciplinary Sciences
Emily C. Moore, Patrick J. Ciccotto, Erin N. Peterson, Melissa S. Lamm, R. Craig Albertson, Reade B. Roberts
Summary: For many vertebrates, a single genetic locus initiates a cascade of developmental sex differences, resulting in adults with two phenotypically distinct sexes. However, species with polygenic sex determination have multiple interacting sex determination alleles, allowing for more than two genotypic sexes. In the cichlid fish Metriaclima mbenjii, polygenic sex determination produces modular variation in morphological and behavioral traits, and the evolution or introgression of a newly acquired sex determiner creates additional axes of phenotypic variation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Fan Zhang, Chao Ning, Ashley Scott, Qiaomei Fu, Rasmus Bjorn, Wenying Li, Dong Wei, Wenjun Wang, Linyuan Fan, Idilisi Abuduresule, Xingjun Hu, Qiurong Ruan, Alipujiang Niyazi, Guanghui Dong, Peng Cao, Feng Liu, Qingyan Dai, Xiaotian Feng, Ruowei Yang, Zihua Tang, Pengcheng Ma, Chunxiang Li, Shizhu Gao, Yang Xu, Sihao Wu, Shaoqing Wen, Hong Zhu, Hui Zhou, Martine Robbeets, Vikas Kumar, Johannes Krause, Christina Warinner, Choongwon Jeong, Yinqiu Cui
Summary: This study presents genomic data from the earliest human remains found in the Dzungarian Basin and Tarim Basin of Xinjiang, revealing a predominantly Afanasievo ancestry in the former and a local ancestry in the latter. The Tarim individuals showed evidence of dairy pastoralism. The findings do not support previous hypotheses about the origin of the Tarim mummies, suggesting a genetically isolated local population in the Tarim Basin.
Article
Genetics & Heredity
Michelle Jonika, Johnathan Lo, Heath Blackmon
Article
Evolutionary Biology
Richard H. Adams, Heath Blackmon, Michael DeGiorgio
Summary: Stochastic models of character trait evolution play a crucial role in evolutionary biology, with recent focus on considering model parameters and probability distributions when quantifying distances between phylogenetic models. By comparing probability distributions induced by two phylogenies, these distances can provide more informative results than traditional approaches based solely on topology or branch length differences. However, current methods are limited to comparing nucleotide substitution and gene tree distribution models, without addressing other trait classes and associated models.
SYSTEMATIC BIOLOGY
(2021)
Review
Genetics & Heredity
James M. Alfieri, Guosong Wang, Michelle M. Jonika, Clare A. Gill, Heath Blackmon, Giridhar N. Athrey
Summary: Single-cell sequencing has revolutionized our understanding of cell diversity, organizational connections, and genotype-phenotype relationships. While most research has been focused on model organisms, applying this technology to non-model organisms can uncover new insights that are inaccessible using traditional model organisms.
Article
Multidisciplinary Sciences
Johnathan Lo, Heath Blackmon
Summary: This study examines the correlation between retrogene survival and changes in genetic linkage. The results suggest that selection on linkage may not be a significant factor in retrogene survival overall, but it might still play a role in the survival of specific retrogenes.
Editorial Material
Ecology
Michelle M. Jonika, James M. Alfieri, Terrence Sylvester, Andrew Riley Buhrow, Heath Blackmon
Article
Ecology
Magnolia W. Morelli, Heath Blackmon, Carl E. Hjelmen
Summary: Karyotypes and chromosome data have been widely used in biology, but are often scattered and difficult to access. Researchers have built two datasets for true flies, providing a public database resource for exploring karyotypes.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Review
Ecology
Katie E. Lotterhos, Matthew C. Fitzpatrick, Heath Blackmon
Summary: The fields of ecology, evolution, and systematics lack standardized principles for evaluating methods, leading to inconsistencies in method testing, ambiguity in limitations, and the risk of misapplication. This review highlights common pitfalls, the benefits of testing methods with simulated data, and best practices for method evaluations. It emphasizes the difference between evaluation and validation and discusses the strengths and limitations of different evaluation metrics.
ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS
(2022)
Review
Biochemistry & Molecular Biology
Zachary B. Hancock, Emma S. Lehmberg, Heath Blackmon
Summary: In this article, we review the evidence for how continuous spatial structure can impact phylogenetic inference. Using complex continuous-space demographic models, we illustrate the impact of spatial structure on gene tree stoichiometry, topological and branch-length variance, network estimation, and species delimitation. We conclude by suggesting how researchers can identify spatial structure in phylogenetic datasets.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Genetics & Heredity
Annabel Perry, Suzanne E. McGaugh, Alex C. Keene, Heath Blackmon
Summary: The growing use of genomics has provided a foundation for identifying genomic and transcriptional differences across species and experimental conditions. Databases containing genomic and functional data have played critical roles, and the study of the Mexican tetra provides a system for understanding convergent evolution.
G3-GENES GENOMES GENETICS
(2022)
Article
Multidisciplinary Sciences
Michael Pitonak, Miriam Aceves, Prakruthi Amar Kumar, Gabrielle Dampf, Peyton Green, Ashley Tucker, Valerie Dietz, Diego Miranda, Sunjay Letchuman, Michelle M. Jonika, David Bautista, Heath Blackmon, Jennifer N. Dulin
Summary: The biological sex of transplanted cells does not significantly affect the outcomes of neural progenitor cell transplantation in spinal cord injury. However, female hosts exhibit a specific immune response to male donor cells. This finding highlights the importance of considering biological sex in future clinical trial designs for cell transplantation.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Jacqueline Smith, James M. Alfieri, Nick Anthony, Peter Arensburger, Giridhar N. Athrey, Jennifer Balacco, Adam Balic, Philippe Bardou, Paul Barela, Yves Bigot, Heath Blackmon, Pavel M. Borodin, Rachel Carroll, Meya C. Casono, Mathieu Charles, Hans Cheng, Maddie Chiodi, Lacey Cigan, Lyndon M. Coghill, Richard Crooijmans, Neelabja Das, Sean Davey, Asya Davidian, Fabien Degalez, Jack M. Dekkers, Martijn Derks, Abigail B. Diack, Appolinaire Djikeng, Yvonne Drechsler, Alexander Dyomin, Olivier Fedrigo, Steven R. Fiddaman, Giulio Formenti, Laurent A. F. Frantz, Janet E. Fulton, Elena Gaginskaya, Svetlana Galkina, Rodrigo A. Gallardo, Johannes Geibel, Almas Gheyas, Cyrill John P. Godinez, Ashton Goodell, Jennifer A. M. Graves, Daren K. Griffin, Bettina Haase, Jian-Lin Han, Olivier Hanotte, Lindsay J. Henderson, Zhuo-Cheng Hou, Kerstin Howe, Lan Huynh, Evans Ilatsia, Erich Jarvis, Sarah M. Johnson, Jim Kaufman, Terra Kelly, Steve Kemp, Colin Kern, Jacob H. Keroack, Christophe Klopp, Sandrine Lagarrigue, Susan J. Lamont, Margaret Lange, Anika Lanke, Denis M. Larkin, Greger Larson, John King N. Layos, Ophelie Lebrasseur, Lyubov P. Malinovskaya, Rebecca J. Martin, Maria Luisa Martin Cerezo, Andrew S. Mason, Fiona M. McCarthy, Michael J. McGrew, Jacquelyn Mountcastle, Christine Kamidi Muhonja, William Muir, Kevin Muret, Terence Murphy, Ismael Ng'ang'a, Masahide Nishibori, Rebecca E. O'Connor, Moses Ogugo, Ron Okimoto, Ochieng Ouko, Hardip R. Patel, Francesco Perini, Maria Ines Pigozzi, Krista C. Potter, Peter D. Price, Christian Reimer, Edward S. Rice, Nicolas Rocos, Thea F. Rogers, Perot Saelao, Jens Schauer, Robert Schnabel, Valerie Schneider, Henner Simianer, Adrian Smith, Mark P. Stevens, Kyle Stiers, Christian Keambou Tiambo, Michele Tixier-Boichard, Anna A. Torgasheva, Alan Tracey, Clive A. Tregaskes, Lonneke Vervelde, Ying Wang, Wesley C. Warren, Paul D. Waters, David Webb, Steffen Weigend, Anna Wolc, Alison E. Wright, Dominic Wright, Zhou Wu, Masahito Yamagata, Chentao Yang, Zhong-Tao Yin, Michelle C. Young, Guojie Zhang, Bingru Zhao, Huaijun Zhou
CYTOGENETIC AND GENOME RESEARCH
(2023)
Article
Ecology
James M. Alfieri, Taryn Johnson, Anna Linderholm, Heath Blackmon, Giridhar N. Athrey
Summary: This study sequenced the DNA of a suspected bird hybrid and confirmed its parentage through analysis. Although the hybrid is not between Numida meleagris and Penelope superciliaris, it still represents the most diverged avian hybrid confirmed with genetic data.
ECOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
James M. Alfieri, Michelle M. Jonika, Jennifer N. Dulin, Heath Blackmon
Summary: In this article, the authors synthesized data from thousands of insect species and used biologically realistic models to infer the tempo and mode of chromosome evolution among insect orders. The results showed significant variation in the rate and pattern of chromosome number evolution among different orders. These findings have important implications for understanding speciation and guiding future genome sequencing studies.
Article
Evolutionary Biology
James M. Alfieri, Reina Hingoranee, Giridhar N. Athrey, Heath Blackmon
Summary: This study investigates the impact of divergence time, domestication, and mismatches in morphology, habitat, and clutch size on reproductive isolation in hybridizing bird species. The findings suggest that divergence time and clutch size are significant predictors of reproductive isolation. Interestingly, domestication is also found to be related to reproductive compatibility after considering phylogeny and addressing potential biases.
JOURNAL OF HEREDITY
(2023)
Article
Biology
Nathan W. Anderson, Carl E. Hjelmen, Heath Blackmon
Article
Biology
Erika Machtinger, Karen C. Poh, Risa Pesapane, Danielle M. Tufts
Summary: Vector-borne diseases, transmitted by insects, are a significant threat to global human and animal health. Their emergence is influenced by factors such as environmental changes, host characteristics, and human behavior. The One Health approach is necessary to comprehensively investigate tick-borne diseases and understand the complex interactions between environmental, animal, and human health.
CURRENT OPINION IN INSECT SCIENCE
(2024)
Article
Biology
Pablo Urbaneja-Bernat, Alejandro Tena, Joel Gonzalez-Cabrera, Cesar Rodriguez-Saona
Summary: This article reviews the potential role of plant guttation as a food source for natural enemies, discussing its nutritional value, effects on insect communities, and potential use in conservation biological control.
CURRENT OPINION IN INSECT SCIENCE
(2024)
Article
Biology
Alina A. Mikhailova, Sarah Rinke, Mark C. Harrison
Summary: The genomes of eusocial insects allow the production and regulation of highly distinct phenotypes, largely independent of genotype. Eusociality has evolved convergently in at least three insect orders, but eusocial phenotypes show remarkable similarity. Increased regulatory complexity and the adaptive evolution of chemical communication are common genomic signatures of eusociality. Colony life itself can shape genomes of divergent taxa in a similar manner.
CURRENT OPINION IN INSECT SCIENCE
(2024)
Article
Biology
Dequn Teng, Wei Zhang
Summary: Butterfly wings, with their rich phenotypic diversity and complex biological functions, serve as a crucial system for studying the genetic basis and evolution of phenotypic diversification. Recent studies have revealed the complex functions and genetic and environmental factors involved in determining wing patterns. These factors lead to inter-specific divergence, genetic polymorphism, and phenotypic plasticity, often controlled by key genes. Gene co-option has also been identified as an important mechanism for functional complexity and evolutionary novelty. However, further research is needed for a systematic and comprehensive understanding.
CURRENT OPINION IN INSECT SCIENCE
(2024)