Article
Fisheries
Shala Hankison, Eric J. Gangloff, Breanna Fry, Alena Arnold, A. J. Lashway, Jenell M. Betts, Sandra D. Otap, Katherine Walter, Makenna Y. Juergens, Alax Crawford
Summary: The study on sailfin molly found that females reliant on stored sperm had fewer offspring, but offspring size and short-term growth rate remained the same. Females may use stored sperm in situations where they cannot access mating opportunities, have mated with a preferred male before, or to maximize egg fertilization.
JOURNAL OF FISH BIOLOGY
(2022)
Article
Fisheries
Chia-Hao Chang, Yu-Chun Wang, Tsung-Han Lee
Summary: This study found that under low temperature, freshwater milkfish exhibit poorer cold tolerance and higher oxidative stress compared to seawater milkfish, leading to apoptosis in hepatocytes. Additionally, during low-temperature acclimation, more apoptosis and impaired liver functions were observed in freshwater milkfish compared to seawater milkfish.
Article
Behavioral Sciences
Sylvia Dimitriadou, Eduarda M. Santos, Darren P. Croft, Ronny van Aerle, Indar W. Ramnarine, Amy L. Filby, Safi K. Darden
Summary: This study quantifies the neuroregulatory response of Trinidadian guppies to cooperation or defection by examining the transcriptional response of the oxytocin gene. The results show that individual responses to social partners' behavior depend on individual's predation threat level and experience.
BEHAVIOURAL BRAIN RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Sean James Buckley, Chris Brauer, Peter J. Unmack, Michael P. Hammer, Luciano B. Beheregaray
Summary: The study on the biogeographic history of the southern pygmy perch in Australia revealed that sea-level changes and hydrological fluctuations played crucial roles in species divergence and the formation of cryptic species. Isolated climatic refugia and fragmentation of waterways were identified as factors maintaining genetic differentiation of intra- and interspecific lineages. The findings suggest that predicted increases in aridification and sea level due to anthropogenic climate change could have significant demographic impacts on species.
Article
Biochemistry & Molecular Biology
Ellen A. Bell, Christopher L. Butler, Claudio Oliveira, Sarah Marburger, Levi Yant, Martin I. Taylor
Summary: This study describes the semi-automated generation of a de novo TE library in a non-model teleost using the EDTA pipeline and DeepTE classifier. The performance of this new pipeline across four TE-based metrics was evaluated using genomic and transcriptomic data, revealing quantitative differences in these metrics and highlighting the significant impact of TE library choice on TE-based estimates in non-model species.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Yu-Ting Lin, Tsung-Han Lee
Summary: This study investigated changes in the expression levels of OSTF1, cortisol levels, and their correlation in the marine inhabitant milkfish. The results showed that ostf1b was the primary gene responding to hypertonic stress, and cortisol concentration increased after transferring milkfish from freshwater to seawater. Additionally, cortisol injection increased the expression of ostf1a and ostf1b.
Article
Ecology
Andrew Furness
Summary: An unexpected interaction between the introduced fish species Poecilia latipinna and humans was observed in Lake Vouliagmeni, Greece, where the fish approached and grazed on the skin of bathing humans. This phenomenon is likely a product of multiple contingencies and unique ecological circumstances.
ENVIRONMENTAL BIOLOGY OF FISHES
(2021)
Article
Biochemistry & Molecular Biology
Fatima Sanchez-Barreiro, Binia De Cahsan, Michael Westbury, Xin Sun, Ashot Margaryan, Claudia Fontsere, Michael W. Bruford, Isa-Rita M. Russo, Daniela C. Kalthoff, Thomas Sicheritz-Ponten, Bent Petersen, Love Dalen, Guojie Zhang, Tomas Marques-Bonet, M. Thomas P. Gilbert, Yoshan Moodley
Summary: The black rhinoceros is a critically endangered species in Africa, with its population and distribution greatly reduced due to hunting, habitat disturbance, and poaching crisis. Genetic and genomic assessments were conducted on museum specimens collected between 1775 and 1981, revealing the historic population structure and evolutionary history. Results indicated that the black rhinoceros had six major historic populations with subpopulations, largely corresponding to geography, and population discontinuities were driven by geographical barriers. This comprehensive historic portrait also provided insights for conservation management strategies.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Ecology
Abbie C. Hay, Jonathan Sandoval-Castillo, Georgina M. Cooke, Ning L. Chao, Luciano B. Beheregaray
Summary: This study examines the role of natural selection in the evolutionary divergence of the Amazonian characin fish. The results suggest that variation in turbidity and pH contribute to adaptive divergence, and genes involved in acid-sensitive ion transport pathways and light-sensitive photoreceptor pathways are associated with this variation.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
Mijke J. van der Zee, James R. Whiting, Josephine R. Paris, Ron D. Bassar, Joseph Travis, Detlef Weigel, David N. Reznick, Bonnie A. Fraser
Summary: This study examines the genomic basis of rapid adaptation in the Trinidadian guppy using population genomics. The results show that guppies transplanted from high-predation environments to low-predation environments rapidly evolve towards the phenotypes of naturally colonized low-predation populations. Genome-wide analysis reveals clear signals of population growth and bottlenecks, as well as a region on chromosome 15 under strong selection. These findings provide remarkable insight into the mechanisms underlying rapid adaptation in this species.
Article
Genetics & Heredity
Yvan Papa, Maren Wellenreuther, Mark A. Morrison, Peter A. Ritchie
Summary: This study generated a highly contiguous genome assembly and isoform-resolved transcriptome of the marine teleost tarakihi, providing a useful resource for population genomics and comparative eco-evolutionary studies in teleosts and related organisms.
G3-GENES GENOMES GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Marvin Choquet, Felix Lenner, Arianna Cocco, Gaelle Toullec, Erwan Corre, Jean-Yves Toullec, Andreas Wallberg
Summary: This study used comparative genomics to investigate the genetic variation and adaptation potential of 20 krill species collected from different oceans. The results showed that Antarctic krill species had lower levels of genetic variation and evolutionary rates, indicating a potentially lower adaptive potential to rapid climate change. Additionally, the study identified several candidate genes associated with adaptive evolution in Antarctic krill.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Review
Microbiology
Awtum M. Brashear, Liwang Cui
Summary: Malaria elimination is a challenging task that includes neglected human malaria parasites. Recent advancements in population genomics have allowed us to gain a better understanding of the biology and epidemiology of these parasites, as well as track their migration and evolutionary response. This knowledge could contribute to the development of effective elimination strategies.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Evolutionary Biology
Andrea Bertram, David Fairclough, Jonathan Sandoval-Castillo, Chris Brauer, Anthony Fowler, Maren Wellenreuther, Luciano B. Beheregaray
Summary: The efficacy of fisheries management strategies depends on carrying out stock assessment and management actions at appropriate spatial scales. This study investigated the population genomics of a heavily exploited snapper species along the Australian coastline to understand population structure, connectivity, and the compatibility of current management practices. The results revealed low genetic differentiation and high connectivity across Western Australia, but also identified genetic discontinuities in certain regions, suggesting a need for a review of current spatial management.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Genetics & Heredity
Lucia Spangenberg, Maria Ines Fariello, Dario Arce, Gabriel Illanes, Gonzalo Greif, Jong-Yeon Shin, Seong-Keun Yoo, Jeong-Sun Seo, Carlos Robello, Changhoon Kim, John Novembre, Monica Sans, Hugo Naya
Summary: The Charruas, an Amerindian group in Uruguay, were extinguished as an ethnic group due to genocide, but their heritage still plays a significant role in the identity of Uruguayans. Genetic studies of Uruguayan individuals with Charruan heritage show evidence of indigenous ancestry, with specific genetic markers indicating interactions with other Amerindian groups. The genomic similarity between Charruas and other Amerindians, as well as their European admixture history, reveal a complex genetic and historical background of Uruguay.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Joaquin C. B. Nunez, Stephen Rong, Alejandro Damian-Serrano, John T. Burley, Rebecca G. Elyanow, David A. Ferranti, Kimberly B. Neil, Henrik Glenner, Magnus Alm Rosenblad, Anders Blomberg, Kerstin Johannesson, David M. Rand
Summary: Studies show that 4% of genes in the barnacle genome undergo balancing selection across the entire range of the species, involving functions such as ion regulation, pain reception, and heat tolerance. The data also reveal complex population structure and high divergence between Atlantic and Pacific populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Joaquin C. B. Nunez, Stephen Rong, David A. Ferranti, Alejandro Damian-Serrano, Kimberly B. Neil, Henrik Glenner, Rebecca G. Elyanow, Bianca R. P. Brown, Magnus Alm Rosenblad, Anders Blomberg, Kerstin Johannesson, David M. Rand
Summary: The northern acorn barnacle is a robust system for studying genetic adaptations to highly heterogeneous environments. A study across various habitats in the North Atlantic basin discovered 382 genomic regions containing SNPs consistently zonated, indicating spatially heterogeneous selection is a general feature for this species. These findings suggest that natural selection can maintain functional genetic variation in such environments.
Article
Biochemistry & Molecular Biology
Martin Kapun, Joaquin C. B. Nunez, Maria Bogaerts-Marquez, Jesus Murga-Moreno, Margot Paris, Joseph Outten, Marta Coronado-Zamora, Courtney Tern, Omar Rota-Stabelli, Maria P. Garcia Guerreiro, Sonia Casillas, Dorcas J. Orengo, Eva Puerma, Maaria Kankare, Lino Ometto, Volker Loeschcke, Banu S. Onder, Jessica K. Abbott, Stephen W. Schaeffer, Subhash Rajpurohit, Emily L. Behrman, Mads F. Schou, Thomas J. S. Merritt, Brian P. Lazzaro, Amanda Glaser-Schmitt, Eliza Argyridou, Fabian Staubach, Yun Wang, Eran Tauber, Svitlana Serga, Daniel K. Fabian, Kelly A. Dyer, Christopher W. Wheat, John Parsch, Sonja Grath, Marija Savic Veselinovic, Marina Stamenkovic-Radak, Mihailo Jelic, Antonio J. Buendia-Ruiz, Maria Josefa Gomez-Julian, Maria Luisa Espinosa-Jimenez, Francisco D. Gallardo-Jimenez, Aleksandra Patenkovic, Katarina Eric, Marija Tanaskovic, Anna Ullastres, Lain Guio, Miriam Merenciano, Sara Guirao-Rico, Vivien Horvath, Darren J. Obbard, Elena Pasyukova, Vladimir E. Alatortsev, Cristina P. Vieira, Jorge Vieira, Jorge Roberto Torres, Iryna Kozeretska, Oleksandr M. Maistrenko, Catherine Montchamp-Moreau, Dmitry Mukha, Heather E. Machado, Keric Lamb, Tania Paulo, Leeban Yusuf, Antonio Barbadilla, Dmitri Petrov, Paul Schmidt, Josefa Gonzalez, Thomas Flatt, Alan O. Bergland
Summary: Utilizing a newly developed bioinformatics pipeline, Drosophila melanogaster's Pool-Seq data is mapped to a hologenome to create the largest genomic data repository to date, called DEST, including 271 population samples from over 100 locations worldwide. This dataset can be used to study spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Karen B. Barnard-Kubow, Dorthe Becker, Connor S. Murray, Robert Porter, Grace Gutierrez, Priscilla Erickson, Joaquin C. B. Nunez, Erin Voss, Kushal Suryamohan, Aakrosh Ratan, Andrew Beckerman, Alan O. Bergland
Summary: This study reveals the dynamic nature of genetic structure and composition in facultative sex, and suggests that variations in reproductive strategies can undergo rapid evolutionary changes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Melissa K. Drown, Douglas L. Crawford, Marjorie F. Oleksiak
Summary: Physiological trait variation plays a crucial role in health, responses to global climate change, and ecological performance. However, we still have limited knowledge about the genes and genomic architectures that define this variation. By studying the relationship between physiological traits and mRNA expression, we can gain insights into the genetic architecture of physiological processes and understand how mRNA expression is related to heritable fitness-related traits.
Article
Evolutionary Biology
Melissa K. Drown, Amanda N. DeLiberto, Nicole Flack, Meghan Doyle, Alexander G. Westover, John C. Proefrock, Sandra Heilshorn, Evan D'Alessandro, Douglas L. Crawford, Christopher Faulk, Marjorie F. Oleksiak
Summary: Genetic data from nonmodel species is important for understanding the ecology and physiology of species and can help with species conservation and management. In this study, researchers used long-read sequencing technology and short-read sequencing technology to assemble the genome of the hardhead silverside fish and examine its population genetics. The results show high population connectivity in this species.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Amanda N. DeLiberto, Melissa K. Drown, Moritz A. Ehrlich, Marjorie F. Oleksiak, Douglas L. Crawford
Summary: Physiology plays a crucial role in determining individual responses to global climate change and species distributions across environments. The responses are driven by temperature on three time scales: acute, acclimatory, and evolutionary. Natural selection influences these responses and reduces interindividual variation towards an optimum. However, the interindividual physiological variation is not well characterized. This study found high variation in physiological traits among individuals and populations, and individual variation in thermal sensitivity reflects different physiological strategies to respond to temperature variation, providing many different adaptive responses to changing environments.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2022)
Article
Ecology
Douglas L. Crawford, Max C. Thompson, Trinity Conn, Madeline Kaufman, Trenton Voytko, Anna M. Merritt, Heather MacKay, Tessa Billings, Yi Chng, Yoel E. Stuart, Marjorie F. Oleksiak
Summary: This study examines the importance of genetic convergence and genetic redundancy in evolution. By studying Anolis carolinensis populations in the Bahamas, it is found that character displacement is supported by both genetic convergence and genetic redundancy. Genetic convergence is demonstrated by 215 SNPs being shared among populations on two competing species islands, while genetic redundancy is shown by these SNPs having different allele frequencies on different islands.
Article
Evolutionary Biology
Melissa K. Drown, Marjorie F. Oleksiak, Douglas L. Crawford
Summary: The evolutionary processes driving physiological trait variation depend on the underlying genomic mechanisms, which are diverse and context dependent. This study examines the relationships between genotype, mRNA expression, and physiological traits to understand the genetic complexity and the impact of gene expression on those traits.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
David M. Rand, Joaquin C. B. Nunez, Shawn Williams, Stephen Rong, John T. Burley, Kimberly B. Neil, Adam N. Spierer, Wilson McKerrow, David S. Johnson, Yevgeniy Raynes, Thomas J. Fayton, Nicholas Skvir, David A. Ferranti, Maya Greenhill Zeff, Amanda Lyons, Naima Okami, David M. Morgan, Kealohanuiopuna Kinney, Bianca R. P. Brown, Anne E. Giblin, Zoe G. Cardon
Summary: Manipulation of host phenotypes by parasites is a strategy for enhancing parasite transmission, and this study found that trematode infection alters the gene expression of its amphipod host, leading to changes in coloration, behavior and immune responses. The study provides new genomic tools and transcriptomic analyses to understand how parasites manipulate host phenotypes.
Correction
Biochemistry & Molecular Biology
Martin Kapun, Joaquin C. B. Nunez, Maria Bogaerts-Marquez, Jesus Murga-Moreno, Margot Paris, Joseph Outten, Marta Coronado-Zamora, Courtney Tern, Omar Rota-Stabelli, Maria P. Garcia Guerreiro, Sonia Casillas, Dorcas J. Orengo, Eva Puerma, Maaria Kankare, Lino Ometto, Volker Loeschcke, Banu S. Onder, Jessica K. Abbott, Stephen W. Schaeffer, Subhash Rajpurohit, Emily L. Behrman, Mads F. Schou, Thomas J. S. Merritt, Brian P. Lazzaro, Amanda Glaser-Schmitt, Eliza Argyridou, Fabian Staubach, Yun Wang, Eran Tauber, Svitlana V. Serga, Daniel K. Fabian, Kelly A. Dyer, Christopher W. Wheat, John Parsch, Sonja Grath, Marija Savic Veselinovic, Marina Stamenkovic-Radak, Mihailo Jelic, Antonio J. Buendia-Ruiz, Maria Josefa Gomez-Julian, Maria Luisa Espinosa-Jimenez, Francisco D. Gallardo-Jimenez, Aleksandra Patenkovic, Katarina Eric, Marija Tanaskovic, Anna Ullastres, Lain Guio, Miriam Merenciano, Sara Guirao-Rico, Vivien Horvath, Darren J. Obbard, Elena Pasyukova, Vladimir E. Alatortsev, Cristina P. Vieira, Jorge Vieira, Jorge Roberto Torres, Iryna Kozeretska, Oleksandr M. Maistrenko, Catherine Montchamp-Moreau, Dmitry V. Mukha, Heather E. Machado, Keric Lamb, Tania Paulo, Leeban Yusuf, Antonio Barbadilla, Dmitri Petrov, Paul Schmidt, Josefa Gonzalez, Thomas Flatt, Alan O. Bergland
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Ecology
Goran Bozinovic, Zuying Feng, Damian Shea, Marjorie F. Oleksiak
Summary: This study investigates the effects of parental pollution exposure on the development and physiology of Fundulus heteroclitus embryos. The results show that embryos from parents in clean estuaries are more sensitive to polluted sediment extracts, displaying morphological deformities and developmental delays. The differences in heart rates among sensitive, resistant, and crossed embryos suggest site-specific adaptive cardiac physiology phenotypes. Genetic expression patterns also indicate maternal deposition of pollutants in the eggs and parental effects on gene expression and metabolic alterations. The study highlights the importance of physiological and metabolic differences during embryonic stages in polluted environments.
BMC ECOLOGY AND EVOLUTION
(2022)