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7. Genome-wide analyses reveal drivers of penguin diversification

Author

Vianna, Juliana A, Fernandes, Flávia AN, Frugone, María José, Figueiró, Henrique V, Pertierra, Luis R, Noll, Daly, Bi, Ke, Wang-Claypool, Cynthia Y, Lowther, Andrew, Parker, Patricia, Le Bohec, Celine, Bonadonna, Francesco, Wienecke, Barbara, Pistorius, Pierre, Steinfurth, Antje, Burridge, Christopher P, Dantas, Gisele PM, Poulin, Elie, Simison, W Brian, Henderson, Jim, Eizirik, Eduardo, Nery, Mariana F, and Bowie, Rauri CK

Subjects
Climate Action, Animals, Antarctic Regions, Australia, Climate Change, Ecosystem, Evolution, Molecular, Genome, Genome-Wide Association Study, New Zealand, Phylogeny, Selection, Genetic, Spheniscidae, penguin, Antarctica, genome, ancestral niche, ancestral distribution
Abstract

Penguins are the only extant family of flightless diving birds. They currently comprise at least 18 species, distributed from polar to tropical environments in the Southern Hemisphere. The history of their diversification and adaptation to these diverse environments remains controversial. We used 22 new genomes from 18 penguin species to reconstruct the order, timing, and location of their diversification, to track changes in their thermal niches through time, and to test for associated adaptation across the genome. Our results indicate that the penguin crown-group originated during the Miocene in New Zealand and Australia, not in Antarctica as previously thought, and that Aptenodytes is the sister group to all other extant penguin species. We show that lineage diversification in penguins was largely driven by changing climatic conditions and by the opening of the Drake Passage and associated intensification of the Antarctic Circumpolar Current (ACC). Penguin species have introgressed throughout much of their evolutionary history, following the direction of the ACC, which might have promoted dispersal and admixture. Changes in thermal niches were accompanied by adaptations in genes that govern thermoregulation and oxygen metabolism. Estimates of ancestral effective population sizes (N e ) confirm that penguins are sensitive to climate shifts, as represented by three different demographic trajectories in deeper time, the most common (in 11 of 18 penguin species) being an increased N e between 40 and 70 kya, followed by a precipitous decline during the Last Glacial Maximum. The latter effect is most likely a consequence of the overall decline in marine productivity following the last glaciation.

Published
2020

10. Cryptic speciation in gentoo penguins is driven by geographic isolation and regional marine conditions : Unforeseen vulnerabilities to global change

Author

Pertierra, Luis R., Segovia, Nicolás I., Noll, Daly, Martinez, Pablo A., Pliscoff, Patricio, Barbosa, Andrés, Aragón, Pedro, Rey, Andrea Raya, Pistorius, Pierre, Trathan, Phil, Polanowski, Andrea, Bonadonna, Francesco, Le Bohec, Céline, Bi, Ke, Wang-Claypool, Cynthia Y., González-Acuña, Daniel, Dantas, Gisele P. M., Bowie, Rauri C. K., Poulin, Elie, and Vianna, Juliana A.

Published
2020

14. More than the eye can see: Genomic insights into the drivers of genetic differentiation in Royal/Macaroni penguins across the Southern Ocean

Author

Frugone, María José, López, María Eugenia, Segovia, Nicolás I., Cole, Theresa L., Lowther, Andrew, Pistorius, Pierre, Dantas, Gisele P.M., Petry, Maria Virginia, Bonadonna, Francesco, Trathan, Phil, Polanowski, Andrea, Wienecke, Barbara, Bi, Ke, Wang-Claypool, Cynthia Y., Waters, Jonathan M., Bowie, Rauri C.K., Poulin, Elie, and Vianna, Juliana A.

Published
2019
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36. Positive selection over the mitochondrial genome and its role in the diversifcation of gentoo penguins in response to adaptation in isolation

Author

Agencia Estatal de Investigación (España), Ministerio de Economía y Competitividad (España), Noll, D., León, F., Brant, D., Pistorius, P., Le Bohec, Céline, de Bonadonna, Francesco, Trathan, P.N., Barbosa, Andrés, Raya Rey, A., Dantas, G.P.M., Bowie, R.C.K., Poulin, E., Vianna, J.A., Agencia Estatal de Investigación (España), Ministerio de Economía y Competitividad (España), Noll, D., León, F., Brant, D., Pistorius, P., Le Bohec, Céline, de Bonadonna, Francesco, Trathan, P.N., Barbosa, Andrés, Raya Rey, A., Dantas, G.P.M., Bowie, R.C.K., Poulin, E., and Vianna, J.A.

Abstract

Although mitochondrial DNA has been widely used in phylogeography, evidence has emerged that factors such as climate, food availability, and environmental pressures that produce high levels of stress can exert a strong influence on mitochondrial genomes, to the point of promoting the persistence of certain genotypes in order to compensate for the metabolic requirements of the local environment. As recently discovered, the gentoo penguins (Pygoscelis papua) comprise four highly divergent lineages across their distribution spanning the Antarctic and sub-Antarctic regions. Gentoo penguins therefore represent a suitable animal model to study adaptive processes across divergent environments. Based on 62 mitogenomes that we obtained from nine locations spanning all four gentoo penguin lineages, we demonstrated lineage-specific nucleotide substitutions for various genes, but only lineage-specific amino acid replacements for the ND1 and ND5 protein-coding genes. Purifying selection (dN/dS < 1) is the main driving force in the protein-coding genes that shape the diversity of mitogenomes in gentoo penguins. Positive selection (dN/dS > 1) was mostly present in codons of the Complex I (NADH genes), supported by two different codon-based methods at the ND1 and ND4 in the most divergent lineages, the eastern gentoo penguin from Crozet and Marion Islands and the southern gentoo penguin from Antarctica respectively. Additionally, ND5 and ATP6 were under selection in the branches of the phylogeny involving all gentoo penguins except the eastern lineage. Our study suggests that local adaptation of gentoo penguins has emerged as a response to environmental variability promoting the fixation of mitochondrial haplotypes in a non-random manner. Mitogenome adaptation is thus likely to have been associated with gentoo penguin diversification across the Southern Ocean and to have promoted their survival in extreme environments such as Antarctica. Such selective processes on the mitochondria

Published
2022

37. Variation among species and populations in bill shape and size in three planktivorous petrels

Author

European Commission, Ministerio de Economía y Competitividad (España), Natural Environment Research Council (UK), German Research Foundation, Institut Polaire Français, Armada de Chile, Agencia Estatal de Investigación (España), Laranjeiro, Maria I., Farré, Marc, Phillips, Richard A., Quillfeldt, Petra, Bonadonna, Francesco, Gémard, Charlene, Daigre, Maximiliano, Suazo, Cristián G., Barbraud, Christophe, Navarro, Joan, European Commission, Ministerio de Economía y Competitividad (España), Natural Environment Research Council (UK), German Research Foundation, Institut Polaire Français, Armada de Chile, Agencia Estatal de Investigación (España), Laranjeiro, Maria I., Farré, Marc, Phillips, Richard A., Quillfeldt, Petra, Bonadonna, Francesco, Gémard, Charlene, Daigre, Maximiliano, Suazo, Cristián G., Barbraud, Christophe, and Navarro, Joan

Abstract

Morphological variation in biological structures may be driven by genetic and environmental factors, such as inter- and intraspecific competition for resources. In seabirds, although the bill is also involved in vocalization, olfaction, sexual selection and defence, the main drivers of high morphological plasticity in bill size and shape appear to relate primarily to diet and thus to niche differentiation. Here, we combined geometric morphometrics and comparisons of linear measurements as a precise tool for measuring shape variation in anatomical features, to investigate the differences among species and populations (island groups) in bill shape of three planktivorous petrels (Antarctic prion Pachyptila desolata, blue petrel Halobaena caerulea and thin-billed prion Pachyptila belcheri). Fieldwork was carried out in South Georgia (54° 0′ S, 38° 3′ W), Falkland (51° 42′ S, 57° 51′ W), Diego Ramírez (56° 31′ S, 68° 44′ W) and Kerguelen (49° 20′ S, 69° 20′ E) Islands, from 2010 to 2021. Results show that the bills of Antarctic prions were more robust and shorter, appropriate for filtering large amounts of small prey. Blue petrels and thin-billed prions had narrower and longer bills, effective for catching and tearing large single prey. Also, Antarctic prions and blue petrels from Kerguelen had longer and narrower bills than conspecifics from other colonies, which could potentially be explained by geographic variation in diet. In conclusion, prey availability and diversity appear to be important factors influencing variation in bill morphology. This study highlights the utility of geometric morphometrics for investigating bill shape variation in seabirds. Nevertheless, further studies are needed to better understand selective pressures leading to morphological variation of biological structures

Published
2022

46. Sensory biology : linking the internal and external ecologies of marine organisms

Author

Weissburg, Marc J., Browman, Howard I., Weissburg, Marc J., Browman, Howard I., Fields, David M., Weissburg, Marc J., Hemmi, Jan M., Zeil, Jochen, Higgs, Dennis M., Johnsen, Sönke, Mead, Kristina S., Mogdans, Joachim, Nevitt, Gabrielle A., Bonadonna, Francesco, Walker, Michael M., and Dennis, Todd E.

Published
2005

48. Front Cover

Author

Frugone, María José, primary, Cole, Theresa L., additional, López, María Eugenia, additional, Clucas, Gemma, additional, Matos‐Maraví, Pável, additional, Lois, Nicolás A., additional, Pistorius, Pierre, additional, Bonadonna, Francesco, additional, Trathan, Phil, additional, Polanowski, Andrea, additional, Wienecke, Barbara, additional, Raya‐Rey, Andrea, additional, Pütz, Klemens, additional, Steinfurth, Antje, additional, Bi, Ke, additional, Wang‐Claypool, Cynthia Y., additional, Waters, Jonathan M., additional, Bowie, Rauri C. K., additional, Poulin, Elie, additional, and Vianna, Juliana A., additional

Published
2021
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