Genomic insights into the secondary aquatic transition of penguins

Abstract

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.

Transcriptomic data reveal divergent paths of chitinase evolution underlying dietary convergence in anteaters and pangolins

“…Chitinase gene family evolution seems to have been strongly influenced by historical contingency events related to gene loss following adaptation to a specific diet (Emerling et al 2018; Janiak et al 2018; Chen and Zhao 2019; Tabata et al 2022). For instance, fossil evidence showing that stem penguins primarily relied on large prey items like fish and squid has been invoked to explain the loss of all functional CHIA genes in all extant penguin species despite the recent specialization of some species towards a chitin-rich crustacean diet (Cole et al 2022). One might therefore wonder why in highly specialized myrmecophagous groups which inherited a depauperate chitinase repertoire, such as pangolins and aardwolves, secondary chitinase duplications did not occur.…”

Evolution and diversification of Mountain voles (Rodentia: Cricetidae)

“…Both coalescent and concatenation methods were used to infer phylogenetic trees. We inferred the best maximum likelihood trees using RAxML v8.2.12 77 with the GTR + GAMMA model from 20 independent tree searches and 500 bootstrap replicates for each gene, and then obtained the final species tree using ASTRAL-III 78 based on the multispecies coalescent model with the bootstrap support of each node being estimated by the multilocus resampling method 79 . SVDquartets (parameters of “eval Quartets = 1e + 6 bootstrap = standard”) implemented in PAUP v4.0a167 80 , 81 was also utilised to estimate the species tree with the same dataset to validate the results.…”

Confocal and Electron Microscopic Structure of the Cornea from Three Species of Penguin

“…However, the shape of the penguin cornea does vary, with the smaller penguins having smaller, more steeply curved corneas [ 3 ]. The most recent transmission (TEM) and scanning (SEM) electron microscopic study of the penguin cornea was performed on what was described as a little penguin Eudyptula minor [ 4 ], although we note that these specimens were obtained in Western Australia while ours came from Auckland, New Zealand and recent evidence suggests that they are different species although of the same genus [ 5 , 6 , 7 , 8 , 9 ]. The cornea of both the former penguin and the Magellanic penguin Spheniscus magellanicus have also been the subject of previous electron micrographic studies [ 2 , 10 , 11 , 12 ].…”

“…The aim of this study was to use confocal microscopy to examine the microstructure of the cornea of three species of penguin, the king Aptenodytes patagonicus , gentoo Pygoscelis papua and little penguins. We undertook this study on three different species partly because these three were those most readily accessible in Auckland but, given their vastly different foraging behaviours, known differences in corneal shape and the long period of independent evolution of each species [ 3 , 9 , 15 , 16 , 17 , 18 , 19 , 20 ], we also wished to look for variation within Spheniscidae, and for a possible correlation with size or diving depth. Because TEM of two of these species, namely the king and gentoo, has not previously been published, following confocal microscopy we undertook that examination on one cornea of each to look for any morphological differences between the three species, bar the obvious one of size [ 4 , 10 , 12 ].…”