Article
Biochemistry & Molecular Biology
J. Andrew DeWoody, Avril M. Harder, Samarth Mathur, Janna R. Willoughby
Summary: The importance of genetic diversity in conservation biology cannot be overstated, as it is closely tied to evolutionary fitness and crucial for conservation efforts. In the Anthropocene, responsible management should prioritize the conservation of ecosystems, communities, populations, individuals, and their underlying genetic diversity.
Article
Agriculture, Dairy & Animal Science
Shantanu Kundu, Tanoy Mukherjee, Ah Ran Kim, Soo-Rin Lee, Abhishek Mukherjee, Won-Kyo Jung, Hyun-Woo Kim
Summary: This study reveals lower genetic diversity and more fragmented habitats in India compared to Sri Lanka for the star tortoise, Geochelone elegans. The findings highlight the need for genetic screening, strict measures against wildlife trafficking, and urgent habitat restoration to protect this highly-threatened species.
Article
Biochemical Research Methods
Sarah S. Ji, Christopher A. German, Kenneth Lange, Janet S. Sinsheimer, Hua Zhou, Jin Zhou, Eric M. Sobel
Summary: TraitSimulation, an open-source Julia package, allows for quick phenotype simulation under various genetic architectures and study designs. Integrated into OpenMendel suite for downstream analyses, it leverages the computational efficiency of Julia and enables flexible trait simulation. By providing more realistic phenotype models, TraitSimulation brings power calculations and diagnostic tools closer to real-world analyses.
BMC BIOINFORMATICS
(2021)
Article
Evolutionary Biology
Bethany A. Zumwalde, Bailie Fredlock, Emily Beckman Bruns, Drew Duckett, Ross A. McCauley, Emma Suzuki Spence, Sean Hoban
Summary: The study reveals that the genetic diversity of the threatened desert oak species is mostly conserved in ex situ populations, with one geographic region showing better conservation than the other. Genetic diversity conservation for the widespread species is lower compared to rarer taxa, and genetic diversity within each garden is influenced by the number of plants and source populations. Overall, measures of geographic and ecological conservation tended to be lower than direct assessment of genetic diversity.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Biodiversity Conservation
Kaylee Rosenberger, Emily Schumacher, Alissa Brown, Sean Hoban
Summary: The study found that proportional sampling to population size captures more genetic diversity when population sizes differ. A relatively modest improvement (1-5% more allelic diversity for most cases) was observed across all parameters tested, except when recent bottlenecks were present. The study also tailored simulations to three IUCN Red List threatened oaks and found similar results as the generic simulations, suggesting that proportional sampling can be used as a useful strategy to create genetically diverse ex situ plant populations for more efficient resource use.
BIOLOGICAL CONSERVATION
(2021)
Editorial Material
Biochemistry & Molecular Biology
Michael Bunce
Summary: When it comes to ancient DNA, people usually think of extinct megafauna, but the study of small vertebrates is often overlooked. This study introduces a minimally destructive method to study the ancient DNA of small vertebrates, focusing on New Zealand geckos. The researchers reconstruct the evolutionary history of these geckos and provide insights into managing remnant populations. This work not only has implications for New Zealand geckos, but also opens up opportunities for biomolecular research on small vertebrate samples in museum collections.
Article
Biodiversity Conservation
Katrin R. Hohwieler, Deidre L. Villiers, Romane H. Cristescu, Celine H. Frere
Summary: Fragmentation of habitat poses a major threat to biodiversity, leading to genetic erosion. A genetic monitoring study on koalas revealed a decrease in genetic diversity, effective population size, and an increase in sub-structuring, relatedness, and inbreeding. The findings highlight the urgent need for mitigation measures to protect this threatened species and similar populations, emphasizing the importance of effective management and genetic erosion monitoring.
CONSERVATION SCIENCE AND PRACTICE
(2022)
Article
Biodiversity Conservation
Ellen Gradl, Theresa A. Lehmair, Peter Poschlod, Christoph Reisch
Summary: This study proposes a new approach for selecting target sites for a network of genetic conservation areas (GCAs), taking into account the current genetic variation. It suggests that the inclusion of further sites is necessary when establishing GCA networks for multiple species. However, it also emphasizes that genetic variation is not the only relevant parameter, and other factors such as property situation, funding availability, and land use history should be considered in the decision-making process.
BIOLOGICAL CONSERVATION
(2022)
Article
Genetics & Heredity
Jakub Skorupski, Johan Michaux, Przemyslaw Smietana
Summary: The meta-analysis aimed to examine the completeness of mtDNA haplotype sampling in recent studies of M. lutreola inter-population genetic diversity, showing a relatively low sample coverage for the Russian population, indicating an urgent need for conservation measures.
Article
Green & Sustainable Science & Technology
Elis Nycander, German Morales-Espana, Lennart Soder
Summary: This paper investigates the possibility of using a power-based version of an economic dispatch model to decrease the model time resolution in the planning of future power systems with high shares of renewable generation. The results show that the power-based model has better agreement with the high-resolution model, especially as the model time step increases.
Article
Ecology
Anusha P. Bishop, E. Anne Chambers, Ian J. Wang
Summary: Genetic diversity is crucial for population viability and adaptation. This study introduces wingen, an r package that calculates genetic diversity maps using genotypic and spatial data. It provides functions for accounting for variation in sample size, creating interpolated maps, and masking irrelevant areas. Tests show that wingen successfully captures genetic diversity variation in landscapes using different sequencing datasets. It is computationally tractable and has applications in conservation prioritization and genetic analyses.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Paula E. Adams, Anna B. Crist, Ellen M. Young, John H. Willis, Patrick C. Phillips, Janna L. Fierst
Summary: The outcrossing species C. remanei can recover from inbreeding, but the recovery is limited by the presence of a large number of segregating deleterious variants in natural populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Linnea Smeds, Hans Ellegren
Summary: When new mutations arise at functional sites, they are more likely to have negative effects on fitness. This is particularly important for the inbred Scandinavian wolf population, which was founded by a small number of wolves in the 1980s and suffers from inbreeding depression. The study reveals that genetic drift and inbreeding in this population have led to an increase in deleterious mutations, but the arrival of immigrants temporarily rescued the genetic load. However, without permanent connectivity to other populations, inbreeding again exposed the population to deleterious mutations, highlighting the importance of gene flow in managing endangered populations.
Article
Biochemistry & Molecular Biology
Liam Quinn, Genis Garcia-Erill, Cindy Santander, Anna Bruniche-Olsen, Xiaodong Liu, Mikkel-Holger S. Sinding, Michael P. P. Heaton, Timothy P. L. Smith, Patricia Pecnerova, Laura D. D. Bertola, Kristian Hanghoj, Malthe Sebro Rasmussen, Deon de Jager, Hans R. R. Siegismund, Anders Albrechtsen, Rasmus Heller, Ida Moltke
Summary: The iconic Cape buffalo has experienced population declines attributed to multiple factors, including the rinderpest pandemic and recent human activity. This study analyzed whole genome sequencing data to assess genetic diversity in Cape buffalo populations. The results indicate that recent inbreeding and colonialism-associated events have significantly impacted the genetic diversity of the southernmost populations.
Article
Biochemistry & Molecular Biology
Shawna J. Zimmerman, Cameron L. Aldridge, Mevin B. Hooten, Sara J. Oyler-McCance
Summary: Habitat fragmentation and degradation have a significant impact on an organism's gene flow and extinction risk. Understanding the effects of landscape composition and scale on gene flow is crucial for conservation decision-making. Using a landscape genetics approach, we identified sagebrush habitat as the primary driver of connectivity for Gunnison sage-grouse.
Article
Zoology
Rocio Alvarez-Varas, Maike Heidemeyer, Cynthia Riginos, Hugo A. Benitez, Eduardo Resendiz, Monica Lara-Uc, Daniel A. Godoy, Juan Pablo Munoz-Perez, Daniela E. Alarcon-Ruales, Gabriela M. Velez-Rubio, Alejandro Fallabrino, Susanna Piovano, Joanna Alfaro-Shigueto, Clara Ortiz-Alvarez, Jeffrey C. Mangel, Damien Esquerre, Patricia Zarate, Carol Medrano, Fabiola Leon Miranda, Felipe Guerrero, Juliana A. Vianna, David Veliz
Summary: In highly mobile marine vertebrates like the green turtle, genetic and phenotypic differentiation patterns are congruent between lineages, with adaptive divergence suggested at fine scales. Connectivity among Pacific foraging grounds may be influenced by ocean surface current temperatures, shaping the genetic structure of C. mydas at broad scales. Factors like vicariance, dispersal, life-history traits, and ecological conditions in foraging grounds have shaped the intraspecific morphology and genetic diversity of this species.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2021)
Article
Ecology
Iva Popovic, Nicolas Bierne, Federico Gaiti, Milos Tanurdzic, Cynthia Riginos
Summary: This study investigates genetic parallelism in multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis, in different regions and with hybridization with a native congener. The results reveal repeatability in differentiation and introgression across genetically distinct lineages, highlighting the impact of demographic histories and pre-introduction introgression on contemporary admixture dynamics. The findings suggest that interspecific introgression history can shape differentiation between colonizing populations and their hybridization with native congeners.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2021)
Article
Fisheries
Lucie Malard, Cynthia Riginos, Katrina McGuigan
Summary: The study investigated skeletal deformities and meristic traits in Bathygobius cocosensis, an intertidal fish species living across the Indo-Pacific region. Results showed that over 87% of individuals exhibited meristic variation and over 70% had at least one type of skeletal deformity, mostly in the caudal fin area. The unexpected prevalence of skeletal deformities suggests that they may be suitable markers to evaluate an individual's stress exposure during development and subsequent fitness effects.
JOURNAL OF FISH DISEASES
(2021)
Article
Ecology
Danielle Davenport, Paul Butcher, Sara Andreotti, Conrad Matthee, Andrew Jones, Jennifer Ovenden
Summary: Monitoring breeding population size of white sharks in east Australia-New Zealand over a few years shows stable and comparable effective breeding number values using genetic estimators, providing insight into conservation effectiveness.
ECOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Joshua A. Thia, Katrina McGuigan, Libby Liggins, Will F. Figueira, Christopher E. Bird, Andrew Mather, Jennifer L. Evans, Cynthia Riginos
Summary: The interaction of selection, gene flow, and drift influences the trajectory of adaptive evolution, with variability in these processes impacting the predictability of microevolutionary outcomes. A study on an intertidal fish species revealed the complex dynamics of genetic and phenotypic variation affected by space, time, and life stage, highlighting both predictable and stochastic patterns in marine systems when considering multiple ecological dimensions. Such findings may be applicable to species with short, complex life cycles, high dispersal potential, and living in heterogeneous environments.
Article
Biochemistry & Molecular Biology
Katharine E. Prata, Cynthia Riginos, Ryan N. Gutenkunst, Kelly R. W. Latijnhouwers, Juan A. Sanchez, Norbert Englebert, Kyra B. Hay, Pim Bongaerts
Summary: Research has found that there is no genetic structure among certain species in mesophotic coral ecosystems and there are hidden cryptic taxa. High gene flow suggests the possibility of connectivity and replenishment among these species. The study also suggests that environmental selection along shallow to mesophotic depth gradients may drive divergence in certain depth-generalist species. The research highlights the importance of gene flow in connecting different taxa within this relatively diverse Caribbean genus.
Article
Biochemistry & Molecular Biology
Belen Jimenez-Mena, Hugo Flavio, Romina Henriques, Alice Manuzzi, Miguel Ramos, Dorte Meldrup, Janette Edson, Snaebjorn Palsson, Gudbjorg Asta Olafsdottir, Jennifer R. Ovenden, Einar Eg Nielsen
Summary: This research presents specific guidelines and considerations for designing capture sequencing experiments for population genetics, focusing on neutral genomic regions and regions subject to selection. The bait design process for three fish species was described, and the performance of the approach was evaluated across historical and modern samples. The supeRbaits R-package, which implements the workflow used for designing the bait sets, is user-friendly and versatile.
MOLECULAR ECOLOGY RESOURCES
(2022)
Review
Biodiversity Conservation
Dianne L. McLean, Luciana C. Ferreira, Jessica A. Benthuysen, Karen J. Miller, Marie-Lise Schlappy, Matthew J. Ajemian, Oliver Berry, Silvana N. R. Birchenough, Todd Bond, Fabio Boschetti, Ann S. Bull, Jeremy T. Claisse, Scott A. Condie, Pierpaolo Consoli, Joop W. P. Coolen, Michael Elliott, Irene S. Fortune, Ashley M. Fowler, Bronwyn M. Gillanders, Hugo B. Harrison, Kristen M. Hart, Lea-Anne Henry, Chad L. Hewitt, Natalie Hicks, Karlo Hock, Kieran Hyder, Milton Love, Peter I. Macreadie, Robert J. Miller, William A. Montevecchi, Mary M. Nishimoto, Henry M. Page, David M. Paterson, Charitha B. Pattiaratchi, Gretta T. Pecl, Joanne S. Porter, David B. Reeves, Cynthia Riginos, Sally Rouse, Debbie J. F. Russell, Craig D. H. Sherman, Jonas Teilmann, Victoria L. G. Todd, Eric A. Treml, David H. Williamson, Michele Thums
Summary: Offshore oil and gas infrastructure has an impact on ecological connectivity in marine habitats, particularly for larvae and mobile animals. However, there is still a lack of knowledge on the specific effects of oil and gas structures on ecological connectivity, which requires further research. When decommissioning oil and gas infrastructure, it is important to consider the impact on species survival, movement, and distribution.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Evolutionary Biology
Ambrocio Melvin A. Matias, Iva Popovic, Joshua A. Thia, Ira R. Cooke, Gergely Torda, Vimoksalehi Lukoschek, Line K. Bay, Sun W. Kim, Cynthia Riginos
Summary: Genomic studies have revealed extensive hidden diversity in reef-building corals, which is highly underestimated in terms of evolutionary and ecological relevance. Additionally, symbiotic algae within coral host species can provide adaptive responses to environmental stress and may contribute to coral genetic variation. This study examines the genetic variation of Acropora tenuis coral host and its associated symbiotic algae across the Great Barrier Reef. The results demonstrate three distinct genetic clusters of coral hosts, associated with latitude and inshore-offshore reef position, while symbiotic algae diversity is influenced by reef location relative to shore.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Ecology
Angela McGaughran, Libby Liggins, Katharine A. Marske, Michael N. Dawson, Lauren M. Schiebelhut, Shane D. Lavery, L. Lacey Knowles, Craig Moritz, Cynthia Riginos
Summary: This article discusses the opportunities and challenges of comparative phylogeography in the genomic age, highlighting the importance of collecting co-distributed species and accruing species-specific ecological knowledge, as well as the availability of bioinformatic skills and user-friendly analytical tools for genomic data analysis.
JOURNAL OF BIOGEOGRAPHY
(2022)
Article
Biodiversity Conservation
Eric D. Crandall, Rachel H. Toczydlowski, Libby Liggins, Ann E. Holmes, Maryam Ghoojaei, Michelle R. Gaither, Briana E. Wham, Andrea L. Pritt, Cory Noble, Tanner J. Anderson, Randi L. Barton, Justin T. Berg, Sofia G. Beskid, Alonso Delgado, Emily Farrell, Nan Himmelsbach, Samantha R. Queeno, Thienthanh Trinh, Courtney Weyand, Andrew Bentley, John Deck, Cynthia Riginos, Gideon S. Bradburd, Robert J. Toonen
Summary: Genetic diversity within species is important for species resilience and conservation policies, but most studies lack the necessary spatial and temporal metadata for reusability and acknowledging sovereignty. We conducted a datathon and found that metadata decayed over time, with successful restoration through papers and online repositories being more effective than contacting authors directly. The rapid decay of metadata availability should prompt updates to data-sharing policies and researcher practices.
CONSERVATION BIOLOGY
(2023)
Article
Biodiversity Conservation
Thomas J. Richards, Katrina McGuigan, J. David Aguirre, Adriana Humanes, Yves-Marie Bozec, Peter J. Mumby, Cynthia Riginos
Summary: Global environmental change is happening rapidly, with coral reefs being one of the most threatened ecosystems. To ensure the survival of wild populations, adaptation is necessary. However, our understanding of the complex ecological and evolutionary dynamics of corals is limited, hindering predictions about their ability to adapt to future conditions.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Environmental Sciences
Graeme S. Cumming, Maja Adamska, Michele L. Barnes, Jon Barnett, David R. Bellwood, Joshua E. Cinner, Philippa J. Cohen, Jennifer M. Donelson, Katharina Fabricius, R. Quentin Grafton, Alana Grech, Georgina G. Gurney, Ove Hoegh-Guldberg, Andrew S. Hoey, Mia O. Hoogenboom, Jacqueline Lau, Catherine E. Lovelock, Ryan Lowe, David J. Miller, Tiffany H. Morrison, Peter J. Mumby, Martin Nakata, John M. Pandolfi, Garry D. Peterson, Morgan S. Pratchett, Timothy Ravasi, Cynthia Riginos, Jodie L. Rummer, Britta Schaffelke, Thomas Wernberg, Shaun K. Wilson
Summary: SDG 14 aims to secure marine sustainability by 2030, and understanding the changing seascape, global actions, and the collaboration between science and society are vital for achieving this goal in the Asia-Pacific region. Through a horizon scan, researchers identified nine emerging research priorities that can contribute to marine sustainability, including understanding seascape evolution, drivers of change, and the costs and benefits to people. Researchers can contribute by developing interdisciplinary understandings, emphasizing equity and justice, and improving knowledge of cross-scale processes.
REGIONAL ENVIRONMENTAL CHANGE
(2023)
Editorial Material
Ecology
Gareth B. Jenkins, Andrew P. Beckerman, Celine Bellard, Ana Benitez-Lopez, Aaron M. Ellison, Christopher G. Foote, Andrew L. Hufton, Marcus A. Lashley, Christopher J. Lortie, Zhaoxue Ma, Allen J. Moore, Shawn R. Narum, Johan Nilsson, Bridget O'Boyle, Diogo B. Provete, Orly Razgour, Loren Rieseberg, Cynthia Riginos, Luca Santini, Benjamin Sibbett, Pedro R. Peres-Neto
Summary: We urge journals to mandate archiving open data in a user-friendly format for readers. Consistent implementation will allow contributors to receive recognition through open data citation and promote scientific advancements.
ECOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Cynthia Riginos, Marlene Jahnke
Summary: Comparative methods are crucial for understanding biodiversity distribution, yet current research primarily focuses on single species. In this study, Zbinden et al. utilized landscape genetics to investigate the landscape genomics of 31 fish species in the White River Basin, revealing the significant impact of stream hierarchy on fish population structure. These findings provide empirical evidence for conservation and fisheries management.