Journal Articles

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    Vulnerability of marine megafauna to global at-sea anthropogenic threats
    (Wiley Periodicals LLC on behalf of Society for Conservation Biology, 2025-11-14) VanCompernolle M; Morris J; Calich HJ; Rodríguez JP; Marley SA; Pearce JR; Abrahms B; Abrantes K; Afonso AS; Aguilar A; Agyekumhene A; Akamatsu T; Åkesson S; Alawa NG; Alfaro-Shigueto J; Anderson RC; Anker-Nilssen T; Arata JA; Araujo G; Arostegui MC; Arrizabalaga H; Arrowsmith LM; Auger-Méthé M; Avila IC; Bailleul F; Barker J; Barlow DR; Barnett A; Barrios-Garrido H; Baylis AMM; Bearzi G; Bejder L; Belda EJ; Benson SR; Berumen ML; Bestley S; Bezerra NPA; Blaison AV; Boehme L; Bograd SJ; Abimbola BD; Bond ME; Borrell A; Bouchet PJ; Boveng P; Braulik G; Braun CD; Brodie S; Bugoni L; Bustamante C; Campana SE; Cárdenas-Alayza S; Carmichael RH; Carroll G; Carter MID; Ceia FR; Cerchio S; Ferreira LC; Chambault P; Chapple TK; Charvet P; Chavez EJ; Chevallier D; Chiaradia A; Chilvers BL; Cimino MA; Clark BL; Clarke CR; Clay TA; Cloyed CS; Cochran JEM; Collins T; Cortes E; Cuevas E; Curnick DJ; Dann P; de Bruyn PJN; de Vos A; Derville S; Dias MP; Diaz-Lopez B; Dodge KL; Dove ADM; Doyle TK; Drymon JM; Dudgeon CL; Dutton PH; Ellenberg U; Elwen SH; Emmerson L; Eniang EA; Espinoza M; Esteban N; Mul E; Fadely BS; Fayet AL; Feare C; Ferguson SH; Feyrer LJ; Finucci B; Florko KRN; Fontes J; Fortuna CM; Fossette S; Fouda L; Frere E; Fuentes MMPB; Gallagher AJ; Borboroglu PG; Garrigue C; Gauffier P; Gennari E; Genov T; Germanov ES; Giménez J; Godfrey MH; Godley BJ; Goldsworthy SD; Gollock M; González Carman V; Gownaris NJ; Grecian WJ; Guzman HM; Hamann M; Hammerschlag N; Hansen ES; Harris MP; Hastie G; Haulsee DE; Hazen EL; Heide-Jørgensen MP; Hieb EE; Higdon JW; Hindell MA; Hinke JT; Hoenner X; Hofmeyr GJG; Holmes BJ; Hoyt E; Huckstadt LA; Hussey NE; Huveneers C; Irvine LG; Jabado RW; Jacoby DMP; Jaeger A; Jagielski PM; Jessopp M; Jewell OJD; Jiménez Alvarado D; Jordan LKB; Jorgensen SJ; Kahn B; Karamanlidis AA; Kato A; Keith-Diagne LW; Kiani MS; Kiszka JJ; Kock AA; Kopf RK; Kuhn C; Kyne PM; Laidre KL; Lana FO; Lander ME; Le Corre M; Lee OA; Leeney RH; Levengood AL; Levenson JJ; Libertelli M; Liu K-M; Lopez Mendilaharsu M; Loveridge A; Lowe CG; Lynch HJ; Macena BCL; Mackay AI
    Marine megafauna species are affected by a wide range of anthropogenic threats. To evaluate the risk of such threats, species’ vulnerability to each threat must first be determined. We build on the existing threats classification scheme and ranking system of the International Union for Conservation of Nature (IUCN) Red List of Threatened Species by assessing the vulnerability of 256 marine megafauna species to 23 at-sea threats. The threats we considered included individual fishing gear types, climate-change-related subthreats not previously assessed, and threats associated with coastal impacts and maritime disturbances. Our ratings resulted in 70 species having high vulnerability (v > 0.778 out of 1) to at least 1 threat, primarily drifting longlines, temperature extremes, or fixed gear. These 3 threats were also considered to have the most severe effects (i.e., steepest population declines). Overall, temperature extremes and plastics and other solid waste were rated as affecting the largest proportion of populations. Penguins, pinnipeds, and polar bears had the highest vulnerability to temperature extremes. Bony fishes had the highest vulnerability to drifting longlines and plastics and other solid waste; pelagic cetaceans to 4 maritime disturbance threats; elasmobranchs to 5 fishing threats; and flying birds to drifting longlines and 2 maritime disturbance threats. Sirenians and turtles had the highest vulnerability to at least one threat from all 4 categories. Despite not necessarily having severe effects for most taxonomic groups, temperature extremes were rated among the top threats for all taxa except bony fishes. The vulnerability scores we provide are an important first step in estimating the risk of threats to marine megafauna. Importantly, they help differentiate scope from severity, which is key to identifying threats that should be prioritized for mitigation.
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    High-coverage genomes to elucidate the evolution of penguins
    (Oxford University Press and BGI, 2019-09-18) Pan H; Cole TL; Bi X; Fang M; Zhou C; Yang Z; Ksepka DT; Hart T; Bouzat JL; Argilla LS; Bertelsen MF; Boersma PD; Bost C-A; Cherel Y; Dann P; Fiddaman SR; Howard P; Labuschagne K; Mattern T; Miller G; Parker P; Phillips RA; Quillfeldt P; Ryan PG; Taylor H; Thompson DR; Young MJ; Ellegaard MR; Gilbert MTP; Sinding M-HS; Pacheco G; Shepherd LD; Tennyson AJD; Grosser S; Kay E; Nupen LJ; Ellenberg U; Houston DM; Reeve AH; Johnson K; Masello JF; Stracke T; McKinlay B; Borboroglu PG; Zhang D-X; Zhang G
    BACKGROUND: Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes. RESULTS: Here we present a novel dataset of 19 high-coverage genomes that, together with 2 previously published genomes, encompass all extant penguin species. We also present a well-supported phylogeny to clarify the relationships among penguins. In contrast to recent studies, our results demonstrate that the genus Aptenodytes is basal and sister to all other extant penguin genera, providing intriguing new insights into the adaptation of penguins to Antarctica. As such, our dataset provides a novel resource for understanding the evolutionary history of penguins as a clade, as well as the fine-scale relationships of individual penguin lineages. Against this background, we introduce a major consortium of international scientists dedicated to studying these genomes. Moreover, we highlight emerging issues regarding ensuring legal and respectful indigenous consultation, particularly for genomic data originating from New Zealand Taonga species. CONCLUSIONS: We believe that our dataset and project will be important for understanding evolution, increasing cultural heritage and guiding the conservation of this iconic southern hemisphere species assemblage.
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    Genomic insights into the secondary aquatic transition of penguins
    (Springer Nature Limited, 2022-07-19) Cole TL; Zhou C; Fang M; Pan H; Ksepka DT; Fiddaman SR; Emerling CA; Thomas DB; Bi X; Fang Q; Ellegaard MR; Feng S; Smith AL; Heath TA; Tennyson AJD; Borboroglu PG; Wood JR; Hadden PW; Grosser S; Bost C-A; Cherel Y; Mattern T; Hart T; Sinding M-HS; Shepherd LD; Phillips RA; Quillfeldt P; Masello JF; Bouzat JL; Ryan PG; Thompson DR; Ellenberg U; Dann P; Miller G; Dee Boersma P; Zhao R; Gilbert MTP; Yang H; Zhang D-X; Zhang G
    Penguins lost the ability to fly more than 60 million years ago, subsequently evolving a hyper-specialized marine body plan. Within the framework of a genome-scale, fossil-inclusive phylogeny, we identify key geological events that shaped penguin diversification and genomic signatures consistent with widespread refugia/recolonization during major climate oscillations. We further identify a suite of genes potentially underpinning adaptations related to thermoregulation, oxygenation, diving, vision, diet, immunity and body size, which might have facilitated their remarkable secondary transition to an aquatic ecology. Our analyses indicate that penguins and their sister group (Procellariiformes) have the lowest evolutionary rates yet detected in birds. Together, these findings help improve our understanding of how penguins have transitioned to the marine environment, successfully colonizing some of the most extreme environments on Earth.