Genome-wide analyses reveal drivers of penguin diversification
Creators
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Vianna, Juliana1
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Fernandes, Flávia A. N.2
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Frugone, María José2
- Figueiró, Henrique V.2
- Pertierra, Luis R.2
- Noll, Daly2
- Bi, Ke2
- Wang-Claypool, Cynthia Y.2
- Lowther, Andrew2
- Parker, Patricia2
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Le Bohec, Celine2
- Bonadonna, Francesco2
- Wienecke, Barbara2
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Pistorius, Pierre2
- Steinfurth, Antje2
- Burridge, Christopher P.2
- Dantas, Gisele P. M.2
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Poulin, Elie2
- Simison, W. Brian2
- Henderson, Jim2
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Eizirik, Eduardo2
- Nery, Mariana F.2
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Bowie, Rauri C. K.2
- 1. Pontifical Catholic University of Chile
- 2. .
Description
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 thatAptenodytesis 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 (Ne) 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 increasedNebetween 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.
Notes
Submission of all the information related to the manuscript of the penguins phylogenome:
- Genomic data: Intron, CDS, UCE, and Mitogenome alignment files for phylogenetic reconstruction and species tree for all data set and without the yellow-eyed penguin genome; and the final dated phylogeny and the BEAST files for UCE and Mitogenome.
- Scripts: Cleaning raw reads: scrubReads.pl; Extracting UCE markers: extractUces.pl; Performing MSA for introns/cds and cleaning the alignment: transExonCapPhyloV3.3.8.pl; Filtering for UCE: FilterByTaxNumber.py and FilterUCE.py; RaxML_NG_Astral III: laucher.py, makeDirs.py and process_runner.py; Predicted Niche Occupancy: PNO_Rscript.txt; Introgression: CreateDfoil_input.py; Natural selection: runEte3_sitemodel_contigs.sh
Funding provided by: Comisión Nacional de Investigación Científica y Tecnológica
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002848
Award Number: GAB PIA ACT172065
Funding provided by: Comisión Nacional de Investigación Científica y Tecnológica
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002848
Award Number: Fondecyt 1150517
Funding provided by: National Science Board
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100005716
Award Number: NSF DEB-1441652
Funding provided by: Instituto Antartico Chileno
Crossref Funder Registry ID:
Award Number: INACH RT_12-14
Funding provided by: French Polar Institute Paul-Emile Victor
Crossref Funder Registry ID:
Award Number: IPEV
Funding provided by: French Polar Institute Paul-Emile Victor
Crossref Funder Registry ID:
Award Number: Progs. 137 and 354
Funding provided by: California Academy os Science
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100015522
Award Number: Lakeside grant
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Introgression-penguins-master.zip
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Additional details
Related works
- Is cited by
- 10.1073/pnas.2006659117 (DOI)