Article
Biochemistry & Molecular Biology
Emily Humble, Jane Hosegood, Gary Carvalho, Mark de Bruyn, Simon Creer, Guy M. W. Stevens, Amelia Armstrong, Ramon Bonfil, Mark Deakos, Daniel Fernando, Niv Froman, Lauren R. Peel, Stephen Pollett, Alessandro Ponzo, Joshua D. Stewart, Sabine Wintner, Rob Ogden
Summary: Understanding population connectivity and genetic diversity is crucial for conservation, but it remains challenging for globally threatened marine megafauna. This study uses a comparative framework to investigate the genetic differentiation and diversity of manta rays, revealing higher connectivity and heterozygosity in oceanic manta rays. The findings also emphasize the potential impact of fisheries on population dynamics.
Article
Ecology
Andrea Barcelo, Jonathan Sandoval-Castillo, Chris J. Brauer, Kerstin Bilgmann, Guido J. Parra, Luciano B. Beheregaray, Luciana M. Moller
Summary: This study conducted a seascape genomics analysis on 214 common dolphins along the southern coast of Australia, and identified five locally-adapted populations with high levels of genomic variation. The study revealed key environmental variables associated with the genomic variation, and suggested that adaptive divergence in common dolphins is related to important metabolic traits.
BMC ECOLOGY AND EVOLUTION
(2022)
Article
Ecology
Abhinav Tyagi, Mihir Godbole, Abi Tamim Vanak, Uma Ramakrishnan
Summary: Human population growth has resulted in fragmented habitats for wildlife, leading to increased interactions between domesticated animals and wild species. Wolf-dog hybridization poses a risk to wolf populations and conservation efforts. Genetic analysis using next-generation sequencing techniques provides evidence of wolf-dog hybrids and the importance of collaborative approaches for monitoring and conservation.
ECOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Jeanne N. Samake, Philip Lavretsky, Isuru Gunarathna, Madison Follis, Joshua I. Brown, Said Ali, Solomon Yared, Tamar E. Carter
Summary: The invasion of Anopheles stephensi in the Horn of Africa poses a significant risk of increased malaria disease burden. By using a genomic approach, this study reveals population differentiation and genetic connectivity within A. stephensi populations in Ethiopia and Somaliland, and identifies a major hub for malaria outbreaks. These findings are valuable for selecting control sites to prevent future malaria outbreaks.
Article
Biochemistry & Molecular Biology
Aglaia Antoniou, Tereza Manousaki, Francisco Ramirez, Alessia Cariani, Rita Cannas, Panagiotis Kasapidis, Antonios Magoulas, Marta Albo-Puigserver, Elena Lloret-Lloret, Jose Maria Bellido, Maria Grazia Pennino, Maria Cristina Follesa, Antonio Esteban, Claire Saraux, Mario Sbrana, Maria Teresa Spedicato, Marta Coll, Costas S. Tsigenopoulos
Summary: By evaluating genetic variation across the entire genome, the study found evidence of local adaptation and population structuring in Sardina pilchardus, which is a highly exploited species. The findings highlight the importance of physical and ecological factors in maintaining population structure, and suggest the need for continuous monitoring under a seascape genomic approach. These results contribute to a deeper understanding of the species' responses to climate change and can aid in predicting future changes.
Article
Biochemistry & Molecular Biology
Stefan Prost, Ana Paula Machado, Julia Zumbroich, Lisa Preier, Sarita Mahtani-Williams, Rene Meissner, Katerina Guschanski, Jaelle C. Brealey, Carlos Rodriguez Fernandes, Paul Vercammen, Luke T. B. Hunter, Alexei V. Abramov, Martin Plasil, Petr Horin, Lena Godsall-Bottriell, Paul Bottriell, Desire Lee Dalton, Antoinette Kotze, Pamela Anna Burger
Summary: Cheetahs, as apex predators, play important roles in ecosystems, but they are facing a precarious conservation status due to habitat loss, human-wildlife conflict, and illegal trafficking. A comprehensive genome-wide analysis of cheetah phylogeography revealed that their genetic differentiation is more complex than previously thought, with distinct genetic characteristics in East African cheetahs compared to Southern African cheetahs. Inbreeding was observed in critically endangered Iranian and Northwestern subspecies, and cheetahs were found to have the lowest genome-wide heterozygosity among big cats. These findings provide valuable information for evidence-based conservation policy decisions and protecting this species in light of ongoing translocations and the threat of illegal trafficking.
Article
Marine & Freshwater Biology
Isabella M. Reeves, John A. Totterdell, Andrea Barcelo, Jonathan Sandoval-Castillo, Kimberley C. Batley, Karen A. Stockin, Emma L. Betty, David M. Donnelly, Rebecca Wellard, Luciano B. Beheregaray, Luciana M. Moller
Summary: Population genomics data has been used to assess the population structure of Australasian killer whales, revealing at least three populations: New Zealand, NWA, and SWA. These populations exhibit moderate levels of genetic diversity, small effective population sizes, and low contemporary migration rates. Mitochondrial DNA analysis suggests the existence of matrilineal societies among killer whales in the region.
MARINE MAMMAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Kyle A. O'Connell, Kevin P. Mulder, Addison Wynn, Kevin de Queiroz, Rayna C. Bell
Summary: This study compared the performance of different sources of genomic DNA for target-capture approach and found that in phylogenetic analyses, all enrichment types for a given specimen clustered together, with capture-based samples clustering together in principal component space, but RADseq samples did not cluster with corresponding capture-based samples.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Agronomy
Pasquale Tripodi, Rosa D'Alessandro, Giovanna Festa, Paola Taviani, Roberto Rea
Summary: This study confirmed the uniqueness and distinctness of the 'Peperone Cornetto di Pontecorvo' variety compared to similar pepper types through morpho-agronomic performance, chemical composition analysis, and genomic fingerprinting. The information obtained will be valuable for the recovery, enhancement, and protection of this local variety.
Article
Fisheries
Jorge Alberto Mares-Mayagoitia, Juan A. De-Anda-Montanez, Ricardo Perez-Enriquez, Paulina Mejia-Ruiz, Jose Luis Gutierrez-Gonzalez, Fausto Valenzuela-Quinonez
Summary: This study used genomic analysis to determine whether the biological units of pink abalone along the western coast of the Baja California Peninsula matched the administrative and stock assessment units. The results showed significant genetic differentiation between the southern and northern regions, contrasting with the current administrative zones.
ICES JOURNAL OF MARINE SCIENCE
(2021)
Article
Biodiversity Conservation
Jessica A. Oswald, Barry Roth, Trevor M. Faske, Julie M. Allen, Cathleen Mestre, Darci Rivers-Pankratz, Kelli Van Norman, Robert P. Guralnick
Summary: This research investigates the diversity of Monadenia in Washington, Oregon, and California, revealing structured units of diversity. Genomic data show widespread admixture and significant differences in genetic differentiation among different morphotypes and species. Further work is needed to evaluate species limits and mechanisms underlying morphological diversity in this group.
CONSERVATION GENETICS
(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
Ecology
F. Gozde Cilingir, Dennis Hansen, Nancy Bunbury, Erik Postma, Richard Baxter, Lindsay Turnbull, Arpat Ozgul, Christine Grossen
Summary: Aldabrachelys gigantea, one of the last two giant tortoise species in the world, faces an uncertain future due to its limited distribution and high vulnerability to climate change. Captive-bred A. gigantea are introduced in rewilding programs, but little is known about the genetic variation and differentiation within and among the islands on Aldabra. Using low-coverage and ddRAD sequencing, the study detected patterns of within-island population structure and found no differentiation between the islands, emphasizing the importance of using genome-wide genetic markers for future management plans.
ECOLOGY AND EVOLUTION
(2022)
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
Biology
Jane M. Edgeloe, Anita A. Severn-Ellis, Philipp E. Bayer, Shaghayegh Mehravi, Martin F. Breed, Siegfried L. Krauss, Jacqueline Batley, Gary A. Kendrick, Elizabeth A. Sinclair
Summary: Polyploidy allows for expansion and adaptation of Poseidon's ribbon weed. A widespread, highly heterozygous polyploid clone was discovered in Shark Bay, Western Australia, making it the largest known clone.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Zoology
Clay M. Wilton, Jeff Beringer, Emily E. Puckett, Lori S. Eggert, Jerrold L. Belant
JOURNAL OF MAMMALOGY
(2016)
Article
Biodiversity Conservation
Emily E. Puckett, Dylan C. Kesler, D. Noah Greenwald
BIOLOGICAL CONSERVATION
(2016)
Article
Biodiversity Conservation
Emily E. Puckett, Lori S. Eggert
BIOLOGICAL CONSERVATION
(2016)
Article
Biology
Emily E. Puckett, Jane Park, Matthew Combs, Michael J. Blum, Juliet E. Bryant, Adalgisa Caccone, Federico Costa, Eva E. Deinum, Alexandra Esther, Chelsea G. Himsworth, Peter D. Keightley, Albert Ko, Ake Lundkvist, Lorraine M. McElhinney, Serge Morand, Judith Robins, James Russell, Tanja M. Strand, Olga Suarez, Lisa Yon, Jason Munshi-South
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2016)
Article
Evolutionary Biology
Emily E. Puckett, Olivia Micci-Smith, Jason Munshi-South
EVOLUTIONARY APPLICATIONS
(2018)
Article
Ecology
Thea V. Kristensen, Emily E. Puckett, Erin L. Landguth, Jerrold L. Belant, John T. Hast, Colin Carpenter, Jaime L. Sajecki, Jeff Beringer, Myron Means, John J. Cox, Lori S. Eggert, Don White, Kimberly G. Smith
Article
Biochemistry & Molecular Biology
Emily E. Puckett, Jason Munshi-South
Article
Ecology
Emily E. Puckett, Eydfinn Magnussen, Liudmila A. Khlyap, Tanja M. Strand, Ake Lundkvist, Jason Munshi-South
Article
Ecology
Jacob J. Burkhart, Emily E. Puckett, Chelsey J. Beringer, Christine N. Sholy, Raymond D. Semlitsch, Lori S. Eggert
ECOLOGY AND EVOLUTION
(2019)
Review
Biochemistry & Molecular Biology
Emily E. Puckett, David Orton, Jason Munshi-South
Article
Ecology
Emily E. Puckett, Emma Sherratt, Matthew Combs, Elizabeth J. Carlen, William Harcourt-Smith, Jason Munshi-South
ECOLOGY AND EVOLUTION
(2020)
Article
Biochemistry & Molecular Biology
Mikkel Winther Pedersen, Bianca De Sanctis, Nedda F. Saremi, Martin Sikora, Emily E. Puckett, Zhenquan Gu, Katherine L. Moon, Joshua D. Kapp, Lasse Vinner, Zaruhi Vardanyan, Ciprian F. Ardelean, Joaquin Arroyo-Cabrales, James A. Cahill, Peter D. Heintzman, Grant Zazula, Ross D. E. MacPhee, Beth Shapiro, Richard Durbin, Eske Willerslev
Summary: Analysis of ancient eDNA has revolutionized our ability to describe biological communities and allows for genomic-scale DNA sequences of closely related species from environmental samples, bringing ancient eDNA into the era of population genomics and phylogenetics.
Article
Ecology
Emily E. Puckett, Sean M. Murphy, Gideon Bradburd
Summary: The study revealed three geographically structured groups in the least chipmunk population and found that the southern subspecies N. m. atristriatus grouped within a unique South subclade. While least chipmunks in the Southwest represent an evolutionary significant unit, subspecies distinctions were not supported, and the listing of the Penasco population as a Distinct Population Segment of N. m. operarius may be warranted. Furthermore, populations with North and West mitogenomes were identified as two additional evolutionary significant units.
ECOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Emily E. Puckett, Isis S. Davis, Dawn C. Harper, Kazumasa Wakamatsu, Gopal Battu, Jerrold L. Belant, Dean E. Beyer, Colin Carpenter, Anthony P. Crupi, Maria Davidson, Christopher S. DePerno, Nicholas Forman, Nicholas L. Fowler, David L. Garshelis, Nicholas Gould, Kerry Gunther, Mark Haroldson, Shosuke Ito, David Kocka, Carl Lackey, Ryan Leahy, Caitlin Lee-Roney, Tania Lewis, Ashley Lutto, Kelly McGowan, Colleen Olfenbuttel, Mike Orlando, Alexander Platt, Matthew D. Pollard, Megan Ramaker, Heather Reich, Jaime L. Sajecki, Stephanie K. Sell, Jennifer Strules, Seth Thompson, Frank van Manen, Craig Whitman, Ryan Williamson, Frederic Winslow, Christopher B. Kaelin, Michael S. Marks, Gregory S. Barsh
Summary: Color variation in large mammals is not well understood, unlike in small mammals. The American black bear exhibits color variation, including a cinnamon morph similar to the brown bear. A single major locus in the TYRP1 gene was identified to affect hair color, and a specific missense alteration was found to decrease pigment production.