A recent study by an international team of scientists* reported specifics of penguin natural history and genetic structure in a paper entitled "Genomic insights into the secondary aquatic transition of penguins," in the journal Nature Communications (13: 3912 (2022).  A significant difference between this study and earlier studies is that this one includes fossil penguins, which make up almost 75% of all penguin species (earlier studies were limited to mitochondrial genes or a few nuclear genes) "combining genomes from all extant and recently-extinct penguin lineages (27 taxa) (Table 1), stratigraphic data from fossil penguins (47 taxa), and morphological and biogeographic data from all species (extant and extinct)."

The data from these analyses support the origin of penguins in New Zealand, originating in stem penguins with extensive local radiation followed by dispersing to Antarctica and South America in multiple invasions of these environments.  Crown penguins, on the other hand, originated in South Africa -- 14Mya from these migrations, followed by dispersal back to New Zealand at least three times, with two of these inferred migrations occurring before the prevailing Antarctica Circumpolar Current had been established (west to east, which would have facilitated these migrations).  The origin of these species coincides with global cooling in the middle Miocene; during at least some of the time periods relevant to penguin evolution there were no polar ice sheets.

These researchers found "incongruities" between phylogenetic trees created by genetic versus conventional morphology-based phylogenies.  They found evidence that rapid speciation of Crown penguins was associated with incomplete lineage sorting (ILS) (due in part to the persistence of polymorphisms across different speciation events) or introgression (transfer of genetic material between related species) resulted from 5% ILS content within ancestors of several penguin species (Spheniscus, Eudyptula, Eudyptes, and several subgroups within Eudyptes).  These results are consistent with closely related penguin species can hybridize in the wild and "provides a temporal framework for this rapid radiation: the four extant Spheniscus taxa are all inferred to have split from one another within the last ~3 Ma, and likewise the nine extant Eudyptes taxa likely split from one another in that same time."

This observed pattern of relatively recent divergence of penguin species within the past 3 million years is a consistent feature among penguin lineages and is correlated with post-speciation introgression events between these populations (events not detected between species that are geographically disparate).  These researchers found "a genomic signature of a period of physical isolation during the Last Glacial Period (LGP) with increased climate fluctuation and environmental uncertainty, followed by postglacial contact and introgression as Earth warmed once again"; similar evidence can be seen in other marine taxa during this period, where penguins and other species moved north away from the South Pole and then back as the earth warmed.

The authors also analogize their historical evidence of climate change during this period with the effects of man-made climate change recently, stating that taxa capable of migration survived better than taxa that were "residential" and foraged close to shore.

Using the integrated evolutionary speed hypothesis (IESH) (which assesses the effects of temperature, water availability, population size, and spatial heterogeneity) these researchers concluded that penguins have the slowest evolutionary rate of all bird species, something these scientists attributed to their "increasing aquatic ecology."  Paradoxically perhaps this perceived evolutionary slowdown could be seen in crown penguins over the first 10 million years of its history but then an uptick in evolutionary rates around 2 million years ago, correlating with the glacial-interglacial cycles during that time has something to do with it.

Turning to genes associated with penguin evolution, these scientists report correlations between phenotypic adaptations (including "their locomotory strategy, thermoregulation, sensory perception, and diet").  They identified three classes of genetic sources of these adaptations:  positively selected genes (PSGs); rapidly evolving genes (REGs); and pseudogenes.  These results showed 15 PSGs and six REGs were penguin-specific adaptations (Fig. 4a) below, five genes containing penguin-specific substitutions, seven pseudogenes, and two gene expansions, illustrated in this figure:

Three of these genes (TBXT and FOXP1, relating to cartilage, tendons, and limb bone and SMAD3, encoding transforming growth factor 3 are related in penguins (and other flightless birds) to "shortening, rigidity, and increased density of the forelimb bones."  Also implicated in limb formation and adaptations was TNMD, a PSG, which the authors speculate may be the cause of "wholesale replacement of penguin distal wing musculature by tendons."  And the authors note that KCNU1 and KCNMA1 genes related to calcium sequestration have been expanded in the genomes of penguins (as well as grebes).

Other genes are implicated in phenotypic features such as densely-packed waterproof feathers, thick skin, and a layer of subcutaneous fat which enables the animals to thermoregulate in cold environments.  These genes include APPL1, TRPC1, EVPL, wherein the APPL1 and TRPC1 genes are involved in glucose levels and fatty acid breakdown through adiponectin; the authors hypothesize these genes promote white adipose fat storage which provide both insulation and an energy reserve.  Another important adaptation is the capacity to withstand hypoxic conditions, and in this regard the transferrin receptor 1 gene TFRC was found to be under positive selection pressure (consistent with expression of this gene in an oxygen-dependent manner even in domesticated cattle).  The FIBB and ANO6 genes, which are involved in blood coagulation, were found to be selected for in species having the capacity for the deepest dives (>500m).  Hemoglobin genes HBA-αA (A140S) and HBB-βA (L87M) had the noted penguin-specific amino acid sequence variations found conserved in all penguin species as were modification in myoglobin genes.  Finally, in this regard a gene that may help widen blood vessels to decrease blood pressure during deep dives, TRPC4, was found to be a PSG.

Vision, particularly low-light vision, is another phenotype hshowing penguin-specific adaptations.  It was known that penguins have only three functional cone photoreceptor types, and the green cone opsin gene RH2, was found in all penguin species to have a 12bp deletion encoding a lysine residue critical for chromophore binding.  These researchers also found specific genetic alterations in red cones associated with blue-shifting the pigment and facilitating a shift in optimum wavelength consistent with ambient underwater light (and having implications for foraging under such conditions).  And deactivation of CYP2J19, a gene that encodes a carotenoid ketolase responsible for producing red oil droplets in avian cone, the authors surmise "likely allows for higher retinal sensitivity when foraging in dim light conditions, as seen in nocturnal owls and kiwis."  Finally, other genes thought responsible for visual sensitivity at low light levels (including TMEM30A (PSG), KCNV2 (REG), CNGB1, and GNB3) show evidence of selection and/or mutations specific to penguins.

Diet is another aspect of penguin lifestyle associated with genetic changes.  This implicates penguin taste sensitivities, and these authors report that penguins have retained the capacity to taste only sour and salty flavors (and the genes associated with these capacities); the genes for sweet, bitter and umami have been lost in all penguin species.  Curiously, according to the authors, the penguin genome contains no active chitinase genes and only one pseudogene, which is inconsistent with a diet comprising crustaceans (because many species are known to consume large amounts of these animals.  The researchers propose (based on fossil evidence) that penguins lost their chitinase genes during ~50 million year interval where they did not consume this prey.

Immune-related genes were also assessed, and 51 PSGs were detected for such genes.  The authors speculate that the selective pressure may be the result of host-pathogen co-evolution.  Examples of such genes include bacterial-recognizing Toll-like receptors TLR4 and TLR5 and within these genes site proximal to the lipopolysaccharide-binding site of TLR4 and the flagellin-binding site of TLR5.  A gene involved in viral RNA detection, IFIT5 is also under positive selection in penguins with positively selected amino acid sites in the protein analogous to similar sites in the human ortholog of this gene.  A similar pattern of selection was found in the penguin gene encoding glycoprotein-mediated hepatitis C viral entry (CD81) with a cluster of positively selected amino acid sites that correspond to similar sites in humans.  Finally, the transferrin gene has undergone positive selection in penguins, which the authors speculate reflects resistance to Corynebacterium infection and diphtheritic stomatitis which are known to cause increased chick mortality.

The authors conclude that penguins acquired most of the genetic adaptations associated with their unique (for birds) aquatic habitat early in their speciation from other birds and that the strong positive selection for these traits is responsible for the low amount of evolutionary change in all penguin taxa.  But their strong adaptation to the colder climate in the peri-South Pole region puts them at risk in the current warming climate trends.  Accordingly these authors suggest that the canary in the global warming coal mine might actually be a penguin.

*Researchers from Demark, Norway, France, the UK, Germany, various European countries, the United States, Argentina, South Africa, New Zealand, China, and Australia reported the results of their studies in a paper entitled "Genetic Insights into the Secondary Aquatic Transition of Penguins," Nature Communications 13: 1-13