Penguin genetics suggests a complex history | McDonnell Boyne Hulbert & Berghof LLP

The penguins are unique among bird species, having lost their ability to fly more than 60 million years ago and adopted a “super-specialized marine body plan” consistent with their unique habitat in the high latitudes of the Southern Hemisphere. Major geological events are thought to be partly responsible, with major climatic oscillations prompting penguins to find ecological refuge and then recolonize former niches.

A recent study by an international team of scientists* detailed the penguin’s natural history and genetic structure in a paper titled “Genetic insights into secondary aquatic transmission of penguins“in the magazine Nature Connections (13:3912 (2022). The big difference between this study and previous studies is that this study includes fossil penguins, which make up approximately 75% of all penguin species (previous studies were limited to mitochondrial genes or a few nuclear genes) Combined genomes of all extant and recently extinct penguin subspecies (27 taxa) (Table 1), stratigraphic data from fossil penguins (47 taxa), morphological and biogeographical data of all species (existing and extinct). “

Table 1a Table 1 b
Data from these analyzes support the origin of New Zealand penguins, which originated in stem penguins with broad local radiation, followed by spread to Antarctica and South America in multiple invasions of these environments. On the other hand, coronal penguins originated in Southern Africa – 14 million of these migrations followed by dispersal back to New Zealand at least three times, with two of these inferred migrations occurring before the establishment of the dominant Antarctic current (from west to east) which would have facilitated these migrations). The origin of this species coincides with the global cooling of the mid-Miocene; During at least some time periods relevant to penguin evolution, there were no polar ice sheets.

These researchers found “inconsistencies” between the phylogenetic tree generated by genetic lineages versus traditional morphology-based patterns. They found evidence that rapid speciation for coronal penguins was associated with incomplete lineage sorting (ILS) (due in part to persistence of polymorphisms across different speciation events) or insertion (transfer of genetic material between related species) that resulted from 5% ILS content within ancestors. many species of penguin (SpheniscusAnd the iodoptulaAnd the adoptise And many subgroups within it adoptise). These findings are consistent with closely related penguin species that can interbreed in the wild and “provide a time frame for this rapid radiation: the four existing species Spheniscus It is inferred that all taxa have separated from each other during the last approximately 3 million, and similarly the remaining nine adoptise The varieties would likely separate from each other at the same time.”

This remarkable pattern of relatively recent divergence of penguin species over the past 3 million years is a consistent feature among penguin lineages and is associated with post-breeding events between these groups (the undetected events between geographically disparate species). These researchers found “a genetic signature of a period of physical isolation during the Last Ice Age (LGP) with increased climate variability and environmental uncertainty, followed by postglacial contact and consolidation as global warming again”; Similar evidence can be seen in other marine taxa during this period, as penguins and other species moved north away from the Antarctic and then back as the Earth warmed.

The authors also compare their historical evidence of climate change during this period with the effects of recent man-made climate change, noting that taxa capable of migration survived better than taxa that were “inhabitable” and fed near shore.

Using the integrated evolutionary velocity hypothesis (IESH) (which assesses the effects of temperature, water availability, population size, and spatial heterogeneity) these researchers conclude that penguins have the slowest evolutionary rate of all bird species, which these scientists attribute to the “increased “. Aquatic ecology.” Paradoxically, this remarkable evolutionary slowdown may be seen in coronal penguins over the first 10 million years of their history, but the higher rates of evolution about 2 million years ago are related to the interglacial glacial cycles during that time.

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Turning to genes associated with penguin evolution, these scientists reported associations between phenotype adaptations (including their “motor strategy, thermoregulation, sensory perception, and diet”). They identified three classes of genetic sources for these adaptations: positively selected genes (PSGs); Rapidly Evolving Genes (REGs); and pseudogenes. These results showed that 15 PSGs and six REGs were penguin-specific adaptations (Fig. 4A) Below, five penguin-specific substitution genes, seven pseudogenes, and two expansion genes, are depicted in this figure:

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Three of these genes (TBXT And the FOXP1related to cartilage, tendons, and limb bones, and SMAD3, encoding transforming growth factor-3 is associated in penguins (and other flightless birds) with “shortening, stiffness, and increased forelimb bone density.” It has also been implicated in limb formation and adaptations TNMD, a PSG, which the authors speculate may be the cause of the “sentence substitution of the muscles of the penguin’s distal flank with tendons.” The authors note that KCNU1 And the KCNMA1 Genes related to calcium sequestration have been expanded in the genomes of penguins (as well as Grubs).

Other genes implicated in phenotypic features such as dense waterproof plumage, thick skin and a layer of subcutaneous fat that enable animals to thermoregulate in cold environments. These genes include APPL1And the TRPC1And the EVPLwhere in APPL1 And the TRPC1 Genes are involved in glucose levels and the breakdown of fatty acids through adiponectin; The authors hypothesize that these genes promote storage of white lipids, which provide both insulation and energy reserves. Another important adaptation is the ability to tolerate hypoxic conditions, and in this regard the transferrin 1 receptor gene TFRC It was found to be subject to positive selection pressure (consistent with the expression of this gene in an oxygen-dependent manner even in domesticated cattle). The vibe And the ANO6 Genes, which are involved in blood clotting, were selected in species that have the ability to dive deeper (>500 m). hemoglobin genes HBA-αA (A140S) and HBB-βA (L87M) contained penguin-specific amino acid sequence variations that were conserved in all penguin species and myoglobin genes were modified. Finally in this regard a gene that may help dilate blood vessels to lower blood pressure during a deep dive, TRPC4was found to be PSG.

Vision, especially low-light vision, is another phenotype that shows adaptations specific to penguins. Penguins were known to have only three types of functional cone photoreceptors, the green cone opsin gene. RH2, was found in all penguin species to have a 12-bp deletion encoding a lysine residue important for chromosomal splicing. These researchers also found specific genetic changes in the red cones that are associated with turning the pigment into blue and facilitating the shift in the optimal wavelength consistent with ambient light underwater (and have implications for foraging under these conditions). and disable CYP2J19, a gene that encodes the carotene ketolase responsible for producing red oil droplets in the cone of birds, the authors believe “likely allows for higher retinal sensitivity when foraging in low light conditions, as seen in nocturnal owls and kiwis.” Finally, other genes have been thought to be responsible for visual sensitivity at low light levels (including TMEM30A (Paris Saint-Germain) , KCNV2 (REG), CNGB1And the GNB3) show evidence of selection and/or mutations specific to penguins.

Diet is another aspect of the penguin’s lifestyle that is linked to genetic changes. This indicates penguin taste sensitivities, and these authors report that penguins retained the ability to taste only sour and salty flavors (and the genes associated with these abilities); The sweet, bitter, and umami genes have been lost in all species of penguins. Curiously, according to the authors, the penguin genome contains no active chitinase genes and only one pseudogene, which is inconsistent with a diet that includes crustaceans (because many species are known to consume large amounts of these animals. The researchers suggest (based on the evidence) The fossils show that penguins lost their chitinase genes during a period of about 50 million years when they did not eat this prey.

Immune-related genes were also evaluated, and 51 PSGs of such genes were detected. The authors speculate that the selective pressure may be a consequence of the coevolution of the pathogen host. Examples of these genes include receptors similar to bacterial recognition TLR4 And the TLR5 Within the site of these genes, close to the lipopolysaccharide binding site TLR4 and flagellin binding site for TLR5. a gene involved in the detection of viral RNA, IFIT5 It also undergoes positive selection in penguins with positively selected amino acid sites in protein similar to similar sites in the human orthologs of this gene. A similar selection pattern was found in the penguin gene that encodes hepatitis C viral entry with glycoprotein (CD81) with a set of positively selected amino acid sites that correspond to similar sites in humans. Finally, the transferrin gene underwent positive selection in penguins, which the authors believe reflects resistance against it. wedge Diphtheria stomatitis infection is known to cause increased chick mortality.

The authors conclude that penguins acquired most of the genetic adaptations associated with their unique aquatic (bird) habitat early in their diversification from other birds and that strong positive selection for these traits is responsible for the low amount of evolutionary change in all penguin species. . But their strong adaptation to the colder Antarctic climate puts them at risk in the current climate trends of warming. Accordingly, these authors suggest that the canary in the coal mine causing global warming may in fact be a penguin.

* Researchers from Demark, Norway, France, the United Kingdom, Germany, various European countries, the United States, Argentina, South Africa, New Zealand, China and Australia report the results of their studies in a paper titled “Genetic Insights in the Secondary Stage. Aquatic Transition of Penguins” Nature Communications 13:1-13

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