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Full-Text Articles in Life Sciences
Variability In Billfish Vertical Distribution And Fishing Interactions Driven By Environmental Conditions In The Eastern Tropical Pacific Ocean, H. E. Blondin, D. E. Haulsee, Ryan Logan, Mahmood Shivji, E. R. Hoffmayer, J. H. Walker, J. M. Dean, E. L. Hazen, L. B. Crowder
Variability In Billfish Vertical Distribution And Fishing Interactions Driven By Environmental Conditions In The Eastern Tropical Pacific Ocean, H. E. Blondin, D. E. Haulsee, Ryan Logan, Mahmood Shivji, E. R. Hoffmayer, J. H. Walker, J. M. Dean, E. L. Hazen, L. B. Crowder
Biology Faculty Articles
Blue marlin (Makaira nigricans) and sailfish (Istiophorus platypterus) are ecologically important predators and valuable species throughout the world’s recreational, commercial, and subsistence fisheries. Comparing multi-species vertical habitat use can inform ecological uncertainties such as inter-species competition, as well as relative vulnerabilities to fishing activities. In this study, we identified key differences in both depth use and which environmental variables drive these selections, which highlights the variability in the catchability both as target species in recreational fisheries and bycatch in commercial fisheries. To understand these two species’ vertical habitat use, we examined depth profiles from 26 sailfish …
Chromosome-Length Assembly Of The Baikal Seal (Pusa Sibirica) Genome Reveals A Historically Large Population Prior To Isolation In Lake Baikal, Aliya Yakupova, Andrey Tomarovsky, Azamat Totikov, Violetta R. Beklemisheva, Maria Logacheva, Polina Perelman, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, Natalya A. Serdyukova, Michael Rayko, Tatiana Bulyonkova, Nikolay Cherkasov, Vladimir Pylev, Vladimir Peterfeld, Aleksey Penin, Elena Balanovska, Alla L. Lapidus, Dna Zoo Consortium, Stephen James O'Brien, Alexander S. Graphodatsky, Klaus-Peter Koepfli, Sergey Kliver
Chromosome-Length Assembly Of The Baikal Seal (Pusa Sibirica) Genome Reveals A Historically Large Population Prior To Isolation In Lake Baikal, Aliya Yakupova, Andrey Tomarovsky, Azamat Totikov, Violetta R. Beklemisheva, Maria Logacheva, Polina Perelman, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, Natalya A. Serdyukova, Michael Rayko, Tatiana Bulyonkova, Nikolay Cherkasov, Vladimir Pylev, Vladimir Peterfeld, Aleksey Penin, Elena Balanovska, Alla L. Lapidus, Dna Zoo Consortium, Stephen James O'Brien, Alexander S. Graphodatsky, Klaus-Peter Koepfli, Sergey Kliver
Biology Faculty Articles
Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat—the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied …
Genetic Population Dynamics Of The Critically Endangered Scalloped Hammerhead Shark (Sphyrna Lewini) In The Eastern Tropical Pacific, Sydney P. Harned, Andrea Bernard, Pelayo Salinas-De-Leon, Marissa Mehlrose, Jenifer Suarez, Yolani Robles, Sandra Bessudo Lion, Felipe Ladino, Andrés López Garo, Ilena Zanella, Kevin A. Feldheim, Mahmood Shivji
Genetic Population Dynamics Of The Critically Endangered Scalloped Hammerhead Shark (Sphyrna Lewini) In The Eastern Tropical Pacific, Sydney P. Harned, Andrea Bernard, Pelayo Salinas-De-Leon, Marissa Mehlrose, Jenifer Suarez, Yolani Robles, Sandra Bessudo Lion, Felipe Ladino, Andrés López Garo, Ilena Zanella, Kevin A. Feldheim, Mahmood Shivji
Biology Faculty Articles
The scalloped hammerhead shark, Sphyrna lewini, is a Critically Endangered, migratory species known for its tendency to form iconic and visually spectacular large aggregations. Herein, we investigated the population genetic dynamics of the scalloped hammerhead across much of its distribution in the Eastern Tropical Pacific (ETP), ranging from Costa Rica to Ecuador, focusing on young-of-year animals from putative coastal nursery areas and adult females from seasonal aggregations that form in the northern Galápagos Islands. Nuclear microsatellites and partial mitochondrial control region sequences showed little evidence of population structure suggesting that scalloped hammerheads in this ETP region comprise a single …
Global Collision-Risk Hotspots Of Marine Traffic And The World’S Largest Fish, The Whale Shark, Freya C. Womersley, Nicolas E. Humphries, Nuno Queiroz, Marisa Vedor, Ivo Da Costa, Miguel Furtado, John P. Tyminski, Katya Abrantes, Gonzalo Araujo, Steffen S. Bach, Adam Barnett, Michael L. Berumen, Sandra Bessudo Lion, Camrin D. Braun, Elizabeth Clingham, Jesse E. M. Cochran, Rafael De La Parra, Stella Diamant, Alistair D. M. Dove, Christine L. Dudgeon, Mark V. Erdmann, Eduardo Espinoza, Richard Fitzpatrick, Jaime González Cano, Jonathan R. Green, Hector M. Guzman, Royale Hardenstine, Abdi Hasan, Fábio H. V. Hazin, Alex R. Hearn, Robert E. Hueter, Mohammed Y. Jaidah, Jessica Labaja, Felipe Ladino, Bruno C. L. Macena, John J. Morris Jr., Bradley M. Norman, Cesar Peñaherrera-Palma, Simon J. Pierce, Lina Maria Quintero, Dení Ramírez-Macías, Samantha D. Reynolds, Anthony J. Richardson, David P. Robinson, Christoph A. Rohner, David R. L. Rowat, Marcus Sheaves, Mahmood Shivji, Abraham B. Sianipar, Gregory B. Skomal, German Soler, Ismail Syakurachman, Simon R. Thorrold, D. Harry Webb, Bradley M. Wetherbee, Timothy D. White, Tyler Clavelle, David A. Kroodsma, Michele Thums, Luciana C. Ferreira, Mark G. Meekan, Lucy M. Arrowsmith, Emily K. Lester, Megan M. Meyers, Lauren R. Peel, Ana M. M. Sequeira, Victor M. Eguiluz, Carlos M. Duarte, David W. Sims
Global Collision-Risk Hotspots Of Marine Traffic And The World’S Largest Fish, The Whale Shark, Freya C. Womersley, Nicolas E. Humphries, Nuno Queiroz, Marisa Vedor, Ivo Da Costa, Miguel Furtado, John P. Tyminski, Katya Abrantes, Gonzalo Araujo, Steffen S. Bach, Adam Barnett, Michael L. Berumen, Sandra Bessudo Lion, Camrin D. Braun, Elizabeth Clingham, Jesse E. M. Cochran, Rafael De La Parra, Stella Diamant, Alistair D. M. Dove, Christine L. Dudgeon, Mark V. Erdmann, Eduardo Espinoza, Richard Fitzpatrick, Jaime González Cano, Jonathan R. Green, Hector M. Guzman, Royale Hardenstine, Abdi Hasan, Fábio H. V. Hazin, Alex R. Hearn, Robert E. Hueter, Mohammed Y. Jaidah, Jessica Labaja, Felipe Ladino, Bruno C. L. Macena, John J. Morris Jr., Bradley M. Norman, Cesar Peñaherrera-Palma, Simon J. Pierce, Lina Maria Quintero, Dení Ramírez-Macías, Samantha D. Reynolds, Anthony J. Richardson, David P. Robinson, Christoph A. Rohner, David R. L. Rowat, Marcus Sheaves, Mahmood Shivji, Abraham B. Sianipar, Gregory B. Skomal, German Soler, Ismail Syakurachman, Simon R. Thorrold, D. Harry Webb, Bradley M. Wetherbee, Timothy D. White, Tyler Clavelle, David A. Kroodsma, Michele Thums, Luciana C. Ferreira, Mark G. Meekan, Lucy M. Arrowsmith, Emily K. Lester, Megan M. Meyers, Lauren R. Peel, Ana M. M. Sequeira, Victor M. Eguiluz, Carlos M. Duarte, David W. Sims
Biology Faculty Articles
Marine traffic is increasing globally yet collisions with endangered megafauna such as whales, sea turtles, and planktivorous sharks go largely undetected or unreported. Collisions leading to mortality can have population-level consequences for endangered species. Hence, identifying simultaneous space use of megafauna and shipping throughout ranges may reveal as-yet-unknown spatial targets requiring conservation. However, global studies tracking megafauna and shipping occurrences are lacking. Here we combine satellite-tracked movements of the whale shark, Rhincodon typus, and vessel activity to show that 92% of sharks’ horizontal space use and nearly 50% of vertical space use overlap with persistent large vessel (>300 …
Why Sequence All Eukaryotes?, Mark Blaxter, John M. Archibald, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Federica Di Palma, Richard Durbin, Scott V. Edwards, Jennifer A.M. Graves, Kevin J. Hackett, Neil Hall, Erich D. Jarvis, Rebecca N. Johnson, Elinor K. Karlsson, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, Kerstin Lindblad-Toh, Jose V. Lopez, Nancy A. Moran, Gene E. Robinson, Oliver A. Ryder, Beth Shapiro, Pamela S. Soltis, Tandy Warnow, Guojie Zhang, Harris A. Lewin
Why Sequence All Eukaryotes?, Mark Blaxter, John M. Archibald, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Federica Di Palma, Richard Durbin, Scott V. Edwards, Jennifer A.M. Graves, Kevin J. Hackett, Neil Hall, Erich D. Jarvis, Rebecca N. Johnson, Elinor K. Karlsson, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, Kerstin Lindblad-Toh, Jose V. Lopez, Nancy A. Moran, Gene E. Robinson, Oliver A. Ryder, Beth Shapiro, Pamela S. Soltis, Tandy Warnow, Guojie Zhang, Harris A. Lewin
Biology Faculty Articles
Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes—about 2 million species—should be sequenced to high quality to produce a …
Seasonal Movements And Habitat Use Of Juvenile Smooth Hammerhead Sharks In The Western North Atlantic Ocean And Significance For Management, Ryan K. Logan, Jeremy Vaudo, Lara L. Sousa, Mark Sampson, Bradley M. Wetherbee, Mahmood S. Shivji
Seasonal Movements And Habitat Use Of Juvenile Smooth Hammerhead Sharks In The Western North Atlantic Ocean And Significance For Management, Ryan K. Logan, Jeremy Vaudo, Lara L. Sousa, Mark Sampson, Bradley M. Wetherbee, Mahmood S. Shivji
Marine & Environmental Sciences Faculty Articles
Upper trophic level predators dramatically impacted by fisheries include the large-bodied hammerhead sharks, which have become species of conservation concern worldwide. Implementing spatial management for conservation of hammerhead populations requires knowledge of temporal distribution patterns and habitat use, identification of essential habitat for protection, and quantification of interactions with human activities. There is little such information for the smooth hammerhead shark, Sphyrna zygaena. We used fin-mounted satellite tags to examine the movements and habitat use of juvenile smooth hammerheads, a demographic segment particularly threatened by exploitation. Six sharks were tagged off the US mid-Atlantic and tracked for 49–441 days …
Seagrasses In The Age Of Sea Turtle Conservation And Shark Overfishing, Michael Heithaus, Teresa Alcoverro, Rohan Arthur, Derek A. Burkholder, Kathryn A. Coates, Marjolijn J. A. Christianen, Nachiket Kelkar, Sarah A. Manuel, Aaron Wirsing, W. Judson Kenworthy, James W. Fourqurean
Seagrasses In The Age Of Sea Turtle Conservation And Shark Overfishing, Michael Heithaus, Teresa Alcoverro, Rohan Arthur, Derek A. Burkholder, Kathryn A. Coates, Marjolijn J. A. Christianen, Nachiket Kelkar, Sarah A. Manuel, Aaron Wirsing, W. Judson Kenworthy, James W. Fourqurean
HCAS Student Articles
Efforts to conserve globally declining herbivorous green sea turtles have resulted in promising growth of some populations. These trends could significantly impact critical ecosystem services provided by seagrass meadows on which turtles feed. Expanding turtle populations could improve seagrass ecosystem health by removing seagrass biomass and preventing of the formation of sediment anoxia. However, overfishing of large sharks, the primary green turtle predators, could facilitate turtle populations growing beyond historical sizes and trigger detrimental ecosystem impacts mirroring those on land when top predators were extirpated. Experimental data from multiple ocean basins suggest that increasing turtle populations can negatively impact seagrasses, …
Habitat Characterization, Distribution, And Areal Extent Of Deep-Sea Coral Ecosystems Off Florida, Southeastern U.S.A., John K. Reed, Charles G. Messing, Brian K. Walker, Sandra Brooke, Thiago B.S. Correa, Myra Brouwer, Tina Udouj, Stephanie Farrington
Habitat Characterization, Distribution, And Areal Extent Of Deep-Sea Coral Ecosystems Off Florida, Southeastern U.S.A., John K. Reed, Charles G. Messing, Brian K. Walker, Sandra Brooke, Thiago B.S. Correa, Myra Brouwer, Tina Udouj, Stephanie Farrington
Marine & Environmental Sciences Faculty Articles
The deep-sea (200-1000 m) seafloor off the southeastern U.S. has a variety of extensive deep-sea coral ecosystem (DSCE) habitats including: deep-water coral mounds; various hard-bottom habitats off Florida including the Miami Terrace, Pourtales Terrace, and deep-water canyons (Agassiz and Tortugas Valleys); and deep island slopes off western Bahamas and northern Cuba. The dominant structure-forming scleractinian corals are Lophelia pertusa and Enallopsammia profunda; other structure-forming taxa include stylasterid corals, gorgonians, black corals, and sponges. This biota is associated with hard-bottom seafloor of variable high-relief topography which can be remotely identified from bathymetric data. NOAA bathymetric contour maps and digital elevation …
Genome Empowerment For The Puerto Rican Parrot – Amazona Vittata, Stephen J. O'Brien
Genome Empowerment For The Puerto Rican Parrot – Amazona Vittata, Stephen J. O'Brien
Biology Faculty Articles
A unique community-funded project in Puerto Rico has launched whole-genome sequencing of the critically endangered Puerto Rican Parrot (Amazona vittata), with interpretation by genome bioinformaticians and students, and deposition into public online databases. This is the first article that focuses on the whole genome of a parrot species, one endemic to the USA and recently threatened with extinction. It provides invaluable conservation tools and a vivid example of hopeful prospects for future genome assessment of so many new species. It also demonstrates inventive ways for smaller institutions to contribute to a field largely considered the domain of large …