Ancient DNA of crested penguins: Testing for temporal genetic shifts in the world’s most diverse penguin clade

Cole, Theresa L.; Rawlence, Nicolas J.; Dussex, Nicolás; Ellenberg, Ursula; Houston, David M.; Mattern, Thomas; Miskelly, Colin M.; Morrison, Kyle W.; Scofield, R. Paul; Tennyson, Alan J. D.; Thompson, David R.; Wood, Jamie R.; Waters, Jonathan M.

doi:10.1016/j.ympev.2018.10.025

Cited by 8 publications

(10 citation statements)

References 53 publications

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“…Divisions between northern rockhopper ( Eudyptes moseleyi ), western rockhopper ( Eudytes chrysocome ), and eastern rockhopper penguins ( Eudyptes filholi ) [3, 7, 8]. Divisions between Fiordland crested ( Eudyptes pachyrhynchus ) and Snares crested penguins ( Eudyptes robustus ) [9, 10]. Divisions between macaroni ( Eudyptes chrysolophus chrysolophus ) and royal penguins ( Eudyptes chrysolophus schlegeli ) [3, 8, 11].…”

Section: Data Descriptionmentioning

confidence: 99%

High-coverage genomes to elucidate the evolution of penguins

Pan

Cole

et al. 2019

GigaScience

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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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Section: Data Descriptionmentioning

confidence: 99%

High-coverage genomes to elucidate the evolution of penguins

Pan

Cole

et al. 2019

GigaScience

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“…In fact, many extant island endemic Eudyptes disperse widely during the non-breeding period: E. pachyrhynchus (breeds only on mainland New Zealand) and E. robustus (breeds only on the Snares) are commonly observed in southern Australia during winter (Woehler 1992;Cole et al 2017;Mattern et al 2018); and E. sclateri (breeds only on the Antipodes Islands) is commonly observed in New Zealand (Robertson et al 2017). As E. warhami is relatively rare in mainland subfossil penguin assemblages (represented by only seven specimens among hundreds of genetically-identified penguin bones [Boessenkool et al 2009a;Rawlence et al 2015a;Grosser et al 2016;Cole et al 2019]), these mainland records fit the pattern that would be expected for non-breeding individuals. In contrast, no Megadyptes antipodes richdalei bones have been detected in mainland subfossil assemblages (Boessenkool et al 2009a; Rawlence et al 2015a;Cole et al 2019).…”

Section: Timing Of Penguin Evolution Linked To Island Emergencementioning

confidence: 62%

“…As E. warhami is relatively rare in mainland subfossil penguin assemblages (represented by only seven specimens among hundreds of genetically-identified penguin bones [Boessenkool et al 2009a;Rawlence et al 2015a;Grosser et al 2016;Cole et al 2019]), these mainland records fit the pattern that would be expected for non-breeding individuals. In contrast, no Megadyptes antipodes richdalei bones have been detected in mainland subfossil assemblages (Boessenkool et al 2009a; Rawlence et al 2015a;Cole et al 2019). This pattern fits with the limited dispersal exhibited by extant Megadyptes populations (Boessenkool et al 2009b).…”

Section: Timing Of Penguin Evolution Linked To Island Emergencementioning

confidence: 62%

“…Most were poorly preserved, but we obtained partial cytochrome oxidase subunit I (COI) sequences from 22, and partial control region (CR) sequences from eight. Phylogenetic analyses of these data identified erect-crested penguin (Eudyptes sclateri) and two other distinct genetic lineages: one corresponding to Eudyptes clade X (Cole et al 2019), and another within the yellow-eyed penguin genus Megadyptes (Fig. S1-S4).…”

Section: Genetic Evidence For Two Extinct Penguin Lineages From the Cmentioning

confidence: 99%

“…Eudyptes warhami bones (cf. E. clade X) excavated from coastal middens demonstrate that the species was also hunted on mainland New Zealand(Cole et al 2019).…”

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Mitogenomes Uncover Extinct Penguin Taxa and Reveal Island Formation as a Key Driver of Speciation

Cole

Ksepka

Tennyson

et al. 2019

Molecular Biology and Evolution

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The emergence of islands has been linked to spectacular radiations of diverse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary diversification of penguins. We test this hypothesis using a fossil-calibrated phylogeny of mitochondrial genomes (mitogenomes) from all extant and recently extinct penguin taxa. Our temporal analysis demonstrates that numerous recent island-endemic penguin taxa diverged following the formation of their islands during the Plio-Pleistocene, including the Galápagos (Galápagos Islands), northern rockhopper (Gough Island), erect-crested (Antipodes Islands), Snares crested (Snares) and royal (Macquarie Island) penguins. Our analysis also reveals two new recently extinct island-endemic penguin taxa from New Zealand’s Chatham Islands: Eudyptes warhami sp. nov. and a dwarf subspecies of the yellow-eyed penguin, Megadyptes antipodes richdalei ssp. nov. Eudyptes warhami diverged from the Antipodes Islands erect-crested penguin between 1.1 and 2.5 Ma, shortly after the emergence of the Chatham Islands (∼3 Ma). This new finding of recently evolved taxa on this young archipelago provides further evidence that the radiation of penguins over the last 5 Ma has been linked to island emergence. Mitogenomic analyses of all penguin species, and the discovery of two new extinct penguin taxa, highlight the importance of island formation in the diversification of penguins, as well as the extent to which anthropogenic extinctions have affected island-endemic taxa across the Southern Hemisphere’s isolated archipelagos.

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