Article
Biochemistry & Molecular Biology
Tabitha Blackwell, Antonia G. P. Ford, Adam G. Ciezarek, Stephanie J. Bradbeer, Carlos A. Gracida Juarez, Alan M. Smith, Benjamin P. Ngatunga, Asilatu Shechonge, Rashid Tamatamah, Graham Etherington, Wilfried Haerty, Federica Di Palma, George F. Turner, Martin J. Genner
Summary: In this study, newly discovered evolutionarily significant populations of Korogwe tilapia from southern Tanzania are threatened by hybridization with invasive Nile tilapia. Genetic analysis shows distinct differences between southern and northern populations of O. korogwe, with evidence of hybrids in southern lakes. This highlights the need for conservation interventions to protect these unique genetic resources.
Article
Biochemistry & Molecular Biology
Laura Duntsch, Annabel Whibley, Pierre de Villemereuil, Patricia Brekke, Sarah Bailey, John G. Ewen, Anna W. Santure
Summary: This study investigates the effects of inbreeding on the fitness of the hihi population. It finds that recent inbreeding has a negative impact on short-term reproductive success, but does not affect other aspects of fitness significantly.
Article
Evolutionary Biology
Jennifer C. C. Nascimento-Schulze, Tim P. P. Bean, Carolina Penaloza, Josephine R. R. Paris, James R. R. Whiting, Alexis Simon, Bonnie A. A. Fraser, Ross D. D. Houston, Nicolas Bierne, Robert P. P. Ellis
Summary: This study developed a multi species medium-density 60K SNP-array for genotyping genetic diversity in the genus Mytilus. It provides a useful tool for investigating ecological and evolutionary processes in these species, as well as for shellfish aquaculture applications such as genetic selection, parentage assignment, inbreeding assessment, and traceability.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Biodiversity Conservation
Catherine R. M. Attard, Jonathan Sandoval-Castillo, Dean M. Gilligan, Peter J. Unmack, Leanne K. Faulks, Luciano B. Beheregaray
Summary: This study demonstrates the application of genomic techniques in detecting hybrid populations of golden perch in the Murray-Darling Basin, southeast Australia, revealing admixture through a genome-wide dataset of 6,862 SNPs. The research suggests that stocking programs may introduce non-endemic ancestry, impacting genetic variation in the wild.
BIODIVERSITY AND CONSERVATION
(2022)
Article
Biochemistry & Molecular Biology
Laura Duntsch, Annabel Whibley, Patricia Brekke, John G. Ewen, Anna W. Santure
Summary: The study on hihi birds revealed that low-density data sets may lead to errors in estimating runs of homozygosity, while low-coverage resequencing and 50K SNP array densities can produce comparable inbreeding results. However, the accuracy of all data sets is heavily influenced by software settings, analysis parameters, and individual sequencing depth.
Article
Multidisciplinary Sciences
Christophe Dufresnes, Nikolay Poyarkov, Daniel Jablonski
Summary: Delimiting and naming biodiversity is crucial for wildlife conservation and research. We propose a standardized workflow for species delimitation based on genomic data, which encourages formal taxonomic naming and description to promote biodiversity awareness.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Ecology
Chase H. Smith, Nathan A. Johnson, Clinton R. Robertson, Robert D. Doyle, Charles R. Randklev
Summary: Population genomics has enhanced our ability to study microevolutionary processes and demographic histories, particularly in imperiled species like freshwater mussels. By using genotype-by-sequencing and mitochondrial sequence data, this study identified conservation units for two imperiled freshwater mussel species and analyzed distribution trends, current status, and factors contributing to population declines. Results showed an increasing trend of occurrence in each conservation unit, suggesting rareness of these species and highlighting the importance of evidence-based recovery planning.
ECOLOGY AND EVOLUTION
(2021)
Article
Biodiversity Conservation
Donna Bradbury, Rachel M. Binks, Margaret Byrne
Summary: Rare species are key targets for biodiversity conservation globally, but limited sample size can hinder assessments of genetic diversity and conservation priority. In this study, SNP analysis was used to address key questions regarding taxonomy, clonality, and genetic diversity in two rare Eucalyptus species, providing important insights for conservation.
BIODIVERSITY AND CONSERVATION
(2021)
Article
Biochemistry & Molecular Biology
Oscar Morton, Brett R. Scheffers, Torbjorn Haugaasen, David P. Edwards
Summary: We assessed the trade volumes of threatened and non-threatened species regulated by CITES and found that non-threatened species dominate the trade. We also discovered a disconnect between trade volumes and changing extinction risk, highlighting potential drawbacks in the current regulation of species trade.
Article
Multidisciplinary Sciences
Carolyn J. Hogg, Kym Ottewell, Peter Latch, Maurizio Rossetto, James Biggs, Andrew Gilbert, Sarah Richmond, Katherine Belov
Summary: Globally, less than 3% of threatened animal species have genomic resources for conservation management. To address this, a consortium in Australia launched the Threatened Species Initiative to develop genomic data and tools for conservation practitioners. The objective is to empower conservation practitioners to access and apply genomic data to their decision-making processes through a web-based portal.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biodiversity Conservation
Sandrine Pavoine, Carlo Ricotta
Summary: Functional traits determine species' responses to environmental change and/or determine species' effects on ecosystem functions. To include functional distinctiveness as a criterion in conservation strategies, we need formal quantification of species' degree of distinctiveness while incorporating extinction risk. Our framework is particularly relevant at the local scale, where species extinctions impact ecosystem functioning and where conservation policies are developed.
BIOLOGICAL CONSERVATION
(2023)
Article
Biodiversity Conservation
Simon J. Verdon, Michael F. Clarke
Summary: Post-fire succession affects the locations and overlap of population hotspots, posing challenges for fire managers in shared locations. The application of fire-age mosaic theory is crucial for species conservation in these areas.
JOURNAL OF APPLIED ECOLOGY
(2022)
Article
Biodiversity Conservation
Dan Xie, Xin-Quan Liu, Ya-Xing Chen, Dan Jiao, Jia-Xin Lou, Xiu-Fei Qiu, Wei-Hua Xu, Zhi-Heng Wang, Jin-Hua Ran, Xiao-Quan Wang
Summary: China is a center of gymnosperm diversity with 195 species, 69 of which are threatened. The conservation status of threatened gymnosperms in China remains largely unknown, with the Western Sichuan Plateau identified as an important conservation priority area. More attention should be given to unprotected threatened gymnosperms and taxonomic studies on species without detailed distribution records.
GLOBAL ECOLOGY AND CONSERVATION
(2021)
Article
Ecology
Friederike C. Bolam, Jorge Ahumada, H. Resit Akcakaya, Thomas M. Brooks, Wendy Elliott, Sean Hoban, Louise Mair, David Mallon, Philip J. K. McGowan, Domitilla Raimondo, Jon Paul Rodriguez, Dilys Roe, Mary B. Seddon, Xiaoli Shen, Simon N. Stuart, James E. M. Watson, Stuart H. M. Butchart
Summary: Preventing human-induced extinctions requires policy commitments to implement targeted recovery actions for threatened species, in addition to comprehensive efforts to mitigate threats to species.
FRONTIERS IN ECOLOGY AND THE ENVIRONMENT
(2023)
Article
Biotechnology & Applied Microbiology
Georgina Samaha, Claire M. Wade, Hamutal Mazrier, Catherine E. Grueber, Bianca Haase
Summary: By using cross-species genome alignment methods, the study successfully identified a large number of variants in cheetah, snow leopard, and Sumatran tiger relative to the domestic cat reference assembly. These variants provided insights into population structure, adaptive traits, evolutionary history, and pathogenesis of heritable diseases. The high degree of synteny among felid genomes allowed for reliable SNV detection and highlighted the potential for improving conservation outcomes.
Article
Biochemistry & Molecular Biology
Stephanie J. Galla, Liz Brown, Yvette (Ngai Tahu Te Hapu o Ngati Waewae) Couch-Lewis, Ilina Cubrinovska, Daryl Eason, Rebecca M. Gooley, Jill A. Hamilton, Julie A. Heath, Samantha S. Hauser, Emily K. Latch, Marjorie D. Matocq, Anne Richardson, Jana R. Wold, Carolyn J. Hogg, Anna W. Santure, Tammy E. Steeves
Summary: Pedigrees, when combined with genomic data, are invaluable for conservation genomic management, addressing pitfalls and allowing for well-informed sampling strategies and quantitative analyses.
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
Biochemistry & Molecular Biology
Laura Duntsch, Patricia Brekke, John G. Ewen, Anna W. Santure
Summary: Sample mix-ups, which occur due to duplication, mislabeling, or swapping of samples, can lead to incorrect genetic data linkage and biased research results. A survey showed that nearly 80% of researchers have encountered sample mix-ups, yet many recent studies in molecular ecology do not report individual assignment checks. To address this issue, a sample verification framework is proposed, utilizing existing metadata to detect and correct sample mix-ups. Application of this framework to a dataset of a threatened bird species resulted in the identification of numerous incorrect genotype-ID associations, highlighting the importance of systematically checking genetic and genomic data sets for accuracy.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Ecology
Brecken C. Robb, Peter J. Olsoy, Jessica J. Mitchell, T. Trevor Caughlin, Donna M. Delparte, Stephanie J. Galla, Marcella R. Fremgen-Tarantino, Jordan D. Nobler, Janet L. Rachlow, Lisa A. Shipley, Jennifer S. Forbey
Summary: Plant communities have complex phenotypic differences that can be further diversified by restoration projects introducing new functional variation. Near-infrared spectroscopy (NIRS) can accurately classify variation within plant taxonomy and phenology, providing a useful tool for selecting seed sources for conservation and monitoring long-term changes in vegetation.
RESTORATION ECOLOGY
(2022)
Article
Ecology
Priscila M. Salloum, Anna W. Santure, Shane D. Lavery, Pierre de Villemereuil
Summary: Genome scans are powerful tools to understand genetic adaptation to future environmental conditions. However, low gene flow and population structure can lead to errors in these scans. This study compared different methods and identified candidate loci associated with environmental factors in a marine mollusc. The results highlight the importance of careful statistical controls in genome scans and suggest that further research is needed to determine the potential of non-model species to adapt to future environments.
JOURNAL OF ANIMAL ECOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Samantha S. Hauser, Stephanie J. Galla, Andrea S. Putnam, Tammy E. Steeves, Emily K. Latch
Summary: Researchers compared six commonly used genome-based relatedness estimators in five captive-bred species. The results showed that different methods, sequencing techniques, and species could lead to variations in genome-based relatedness estimates, indicating the lack of an ideal estimator. For new datasets, it is recommended to evaluate the most appropriate genome-based relatedness estimator based on the correlation with known relationships in the pedigree and the precision of known first-order relationships. These recommendations are broadly applicable to conservation breeding programs and in situ wildlife management.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Zoology
Stefanie Grosser, Ludovic Dutoit, Yasmin Foster, Fiona Robertson, Andrew E. Fidler, Denise Martini, Michael Knapp, Bruce C. Robertson
Summary: Recent genomic evidence suggests that kea (Nestor notabilis) may have impaired vision in the green region of the electromagnetic spectrum due to a non-functional gene. This could have unexpected consequences for kea conservation as it may affect their perception and interaction with green-dyed baits. However, further analysis reveals that the previously reported premature stop codon is likely an assembly error and the RH2 gene is functional in all three species of New Zealand parrots.
NEW ZEALAND JOURNAL OF ZOOLOGY
(2023)
Article
Multidisciplinary Sciences
Timothee Bonnet, Michael B. Morrissey, Pierre de Villemereuil, Susan C. Alberts, Peter Arcese, Liam D. Bailey, Stan Boutin, Patricia Brekke, Lauren J. N. Brent, Glauco Camenisch, Anne Charmantier, Tim H. Clutton-Brock, Andrew Cockburn, David W. Coltman, Alexandre Courtiol, Eve Davidian, Simon R. Evans, John G. Ewen, Marco Festa-Bianchet, Christophe de Franceschi, Lars Gustafsson, Oliver P. Honer, Thomas M. Houslay, Lukas F. Keller, Marta Manser, Andrew G. McAdam, Emily McLean, Pirmin Nietlisbach, Helen L. Osmond, Josephine M. Pemberton, Erik Postma, Jane M. Reid, Alexis Rutschmann, Anna W. Santure, Ben C. Sheldon, Jon Slate, Celine Teplitsky, Marcel E. Visser, Bettina Wachter, Loeske E. B. Kruuk
Summary: This study analyzed long-term data from 19 wild bird and mammal populations and found that additive genetic variance in relative fitness is often substantial and, on average, twice that of previous estimates. These rates of contemporary adaptive evolution can affect population dynamics and suggest that natural selection has the potential to partly mitigate effects of current environmental change.
Article
Ecology
Nicholas J. Foster, Richard F. Maloney, Philip J. Seddon, Mariano Rodriguez-Recio, Yolanda van Heezik
Summary: This study aims to assess whether high-elevation landforms can limit the movements of invasive small mammals and improve the success of eradication programs. Based on species' distributions and spatial predictions, the researchers identified landforms that can act as dispersal barriers. The findings suggest that high-elevation landforms have the potential to significantly enhance the effectiveness of eradication programs by restricting the movement of target species.
Article
Biochemistry & Molecular Biology
Stephanie J. Galla, Carlos Dave C. Dumaguit, John M. A. Wojahn, Stephen Novak, Marcelo Serpe, Peggy Martinez, Sven Buerki
Summary: Severe drought conditions and extreme weather events are increasing globally, posing a threat to native plant communities and ecosystems. This study aimed to broaden our understanding of genome-to-phenome (G2P) connections in drought-stressed plants and identify focal taxa for future research. The analysis revealed gaps in G2P research literature and database connectivity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biodiversity Conservation
Stephanie J. Galla, Cinnamon S. Mittan-Moreau, Soraia Barbosa
Summary: Conservation and the Genomics of Populations is an influential textbook that explores the history of conservation genetics and the application of genomics. Although some chapters require advanced genetic theory, the textbook serves as a valuable reference for conservation geneticists and upper level students.
CONSERVATION GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Laura Duntsch, Annabel Whibley, Pierre de Villemereuil, Patricia Brekke, Sarah Bailey, John G. Ewen, Anna W. Santure
Summary: This study investigates the effects of inbreeding on the fitness of the hihi population. It finds that recent inbreeding has a negative impact on short-term reproductive success, but does not affect other aspects of fitness significantly.
Article
Biochemistry & Molecular Biology
Natalie J. Forsdick, Jana Wold, Anton Angelo, Francois Bissey, Jamie Hart, Mitchell Head, Libby Liggins, Dinindu Senanayake, Tammy E. Steeves
Summary: This article emphasizes the importance of careful and considered data management in the context of increasing accessibility to large-scale biodiversity genomic datasets. It recognizes the challenges associated with managing such datasets and provides guidance and resources for biodiversity genomics researchers.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Ecology
Joseph Guhlin, Marissa F. Le Lec, Jana Wold, Emily Koot, David Winter, Patrick J. Biggs, Stephanie J. Galla, Lara Urban, Yasmin Foster, Murray P. Cox, Andrew Digby, Lydia R. Uddstrom, Daryl Eason, Deidre Vercoe, Tane Davis, Jason T. Howard, Erich D. Jarvis, Fiona E. Robertson, Bruce C. Robertson, Neil J. Gemmell, Tammy E. Steeves, Anna W. Santure, Peter K. Dearden
Summary: The study investigated the genetic variation and phenotypic influences in the critically endangered kakapo parrot using whole-genome sequence data and phenotype data. Associations were found between genic regions and traits such as growth and disease susceptibility. The study also showed that active management has maintained genetic diversity and evolutionary potential in the species. The findings provide insights for future conservation management decisions for the kakapo.
NATURE ECOLOGY & EVOLUTION
(2023)
