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[dinosaur] Penguin genome-wide analyses show crown-group origins + owl nocturnal adaptation evolution




Ben Creisler
bcreisler@gmail.com

New avian papers:


Juliana A. Vianna, FlÃvia A. N. Fernandes, MarÃa Josà Frugone, Henrique V. FigueirÃ, Luis R. Pertierra, Daly Noll, Ke Bi, Cynthia Y. Wang-Claypool, Andrew Lowther, Patricia Parker, Celine Le Bohec, Francesco Bonadonna, Barbara Wienecke, Pierre Pistorius, Antje Steinfurth, Christopher P. Burridge, Gisele P. M. Dantas, Elie Poulin, W. Brian Simison, Jim Henderson, Eduardo Eizirik, Mariana F. Nery, and Rauri C. K. Bowie (2020)
Genome-wide analyses reveal drivers of penguin diversification.
Proceedings of the National Academy of Sciences (advance online publication)
doi: Âhttps://doi.org/10.1073/pnas.2006659117
https://www.pnas.org/content/early/2020/08/12/2006659117
This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2006659117/-/DCSupplemental.

Free pdf:
https://www.pnas.org/content/pnas/suppl/2020/08/12/2006659117.DCSupplemental/pnas.2006659117.sapp.pdf

Significance

Penguins have long been of interest to scientists and the general public, but their evolutionary history remains unresolved. Using genomes, we investigated the drivers of penguin diversification. We found that crown-group penguins diverged in the early Miocene in Australia/New Zealand and identified Aptenodytes (emperor and king penguins) as the sister group to all other extant penguins. Penguins first occupied temperate environments and then radiated to cold Antarctic waters. The Antarctic Circumpolar Currentâs (ACC) intensification 11.6 Mya promoted penguin diversification and geographic expansion. We detected interspecies introgression among penguins, in some cases following the direction of the ACC, and identified genes acting on thermoregulation, oxygen metabolism, and diving capacity that underwent adaptive evolution as they progressively occupied more challenging thermal niches.

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 (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 increased Ne 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.

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News:

Penguins are Aussies. Or are they Kiwis?

https://news.berkeley.edu/2020/08/17/penguins-are-aussies-or-are-they-kiwis/



https://www.npr.org/2020/08/17/903291117/where-did-penguins-come-from-scientists-say-its-not-antarctica


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Not yet mentioned:

Free pdf:

Pamela EspÃndola-HernÃndez, Jakob C Mueller, Martina Carrete, Stefan Boerno & Bart Kempenaers (2020)
Genomic evidence for sensorial adaptations to a nocturnal predatory lifestyle in owls.
Genome Biology and Evolution, evaa166
doi: https://doi.org/10.1093/gbe/evaa166
https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evaa166/5889951


Owls (Strigiformes) evolved specific adaptations to their nocturnal predatory lifestyle, such as asymmetrical ears, a facial disc, and a feather structure allowing silent flight. Owls also share some traits with diurnal raptors and other nocturnal birds, such as cryptic plumage patterns, reversed sexual size dimorphism and acute vision and hearing. The genetic basis of some of these adaptations to a nocturnal predatory lifestyle has been studied by candidate gene approaches, but rarely with genome-wide scans. Here, we used a genome-wide comparative analysis to test for selection in the early history of the owls. We estimated the substitution rates in the coding regions of twenty bird genomes, including eleven owls of which five were newly sequenced. Then, we tested for functional overrepresentation across the genes that showed signals of selection. In the ancestral branch of the owls, we found traces of positive selection in the evolution of genes functionally related to visual perception, especially to phototransduction, and to chromosome packaging. Several genes that have been previously linked to acoustic perception, circadian rhythm and feather structure also showed signals of an accelerated evolution in the origin of the owls. We discuss the functions of the genes under positive selection and their putative association with the adaptation to the nocturnal predatory lifestyle of the owls.


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