Scientists “resurrect” ancient proteins to understand how penguins can hold their breath for so long

Unraveling the evolutionary changes to the hemoglobin protein in penguins.

The study of evolution is sometimes described as “just” a historical science, in comparison to the “superior” experimental sciences. This characterization – popular among creationists – is obviously plain poppycock. Although evolutionary biologists study the history of life on Earth, they use a variety of tools, including experiments. One of the most exciting experimental approaches is the resurrection of ancient proteins to understand how they might have functioned in the ancestors of modern species. A recent study in the journal PNAS provides a beautiful example of this strategy. Researchers reconstructed the hemoglobin protein of the common ancestor of penguins and their non-diving relatives to investigate how this protein has changed over millions of years of evolution.

Ancient Proteins

As you probably know from nature documentaries, penguins dive to great depths to find food. These deep dives require an efficient use of oxygen. Here, the protein hemoglobin plays an important role by binding to oxygen and carrying it to certain tissues. Experimental measurements already showed that hemoglobin in several penguin species has a higher oxygen-binding affinity compared to other bird species. This feature could have evolved in a number of ways: (1) penguins might have evolved an increased affinity for oxygen, (2) non-diving birds might have evolved a decreased affinity for oxygen, or (3) the change happened in both direction, namely increased affinity in penguins and decreased affinity in non-diving birds. To discriminate between these three options, the researchers reconstructed the hemoglobin of the common ancestor of penguins (which they called AncSphen) and the hemoglobin of the common ancestor of penguins and their non-diving relatives (AncPro).

Attentative readers might remark that the non-diving relatives in this scheme – the order Procellariiformes – also dive for food. However, these birds do not perform the extremely deep dives that penguins do.

A phylogenetic overview of the ancient proteins that the researchers reconstructed: AncSphen represents the ancestral condition in penguins while AncPro goes even further back in time to the common ancestor of penguins and non-diving birds. From: Signore et al. (2021).

Bohr Effect

Experiments with the two resurrected proteins – AncSphen and AncPro – revealed that AncSphen has a significantly higher affinity for binding oxygen compared to AncPro. This suggests that penguins have evolved an increased oxygen-binding affinity whereas non-diving birds probably experienced little changes (which fits with scenario 1 mentioned above).

Next, the researchers took a closer look at the role of cofactors, which are chemical compounds that can improve the functioning of proteins. Further experiments revealed that, when cofactors were added to the mix, AncSphen responded two times stronger to changes in pH than AncPro. At lower pH, AncSphen showed a decreased affinity for binding oxygen, releasing it more easily. This particular response to pH – known as the Bohr effect – might compensate for the high oxygen-binding affinity of hemoglobin penguins when it has to unload oxygen at certain tissues.

The addition of cofactors (grey bars) at different pH-levels shows a stronger response in AncSphen compared to AncPro. This Bohr effect allows hemoglobin in penguins to release oxygen more efficiently in acidic tissues. Adapted from: Signore et al. (2021).

The Journey of an Oxygen Molecule

To understand how all of this works, imagine being a oxygen molecule in the blood vessel of a penguin. You have just entered the lungs and become tightly bound to hemoglobin. As you are carried around the body, you wonder how this hemoglobin will ever let you go. Its oxygen-binding affinity is so strong that you cannot escape. However, as the pH starts to drop in the muscle tissue, you feel the grip of the hemoglobin loosening. Once the pH is low enough, you are released and can move into a muscle cell. In other words, the Bohr effect allows hemoglobin to unload its oxygen in acid tissues, resulting in a more efficient oxygen transport around the body.

An amazing adaptation that we managed to understand using an experimental approach. Keep that in mind when someone tells you that evolutionary biology is “just” a historical science.

References

Signore, A. V., Tift, M. S., Hoffmann, F. G., Schmitt, T. L., Moriyama, H., & Storz, J. F. (2021). Evolved increases in hemoglobin-oxygen affinity and the Bohr effect coincided with the aquatic specialization of penguins. Proceedings of the National Academy of Sciences, 118(13), e2023936118.

Featured image: Gentoo Penguin (Pygoscelis papua) © Ken Funakoshi | Wikimedia Commons

How convincing is the evidence to split the Gentoo Penguin into four species?

A critical look at the genetic and morphological data supporting this taxonomic proposal.

Taxonomy is often in flux. As new data are collected or novel methods are being developed, the classification of certain sections on the Tree of Life might change. For example, a recent study in the journal Ecology and Evolution presented morphometric and genetic evidence to split the Gentoo Penguin (Pygoscelis papua) into four distinct species. Last year, this study attracted some media attention (including the BBC and the Oceanographic Magazine), but I remained somewhat skeptical about this taxonomic revision. I added the paper to my writing-list where it gathered dust from several months (there were so many other interesting papers to cover on the blog). Now, it has finally resurfaced and we can assess the evidence. How strong is the case for four species of Gentoo Penguin?

Genetic Lineages

In recent years, taxonomy has become more pluralistic, combining several lines of evidence to support taxonomic decisions (see for example this blog post on larks). The researchers in the penguin study also took an integrative approach and collected genetic and morphological data. The genetic analyses – based on more than 10,000 markers – pointed to four clearly distinct lineages, corresponding to populations from several islands (i.e. Falklands, South Georgia Island, South Shetland Islands + Western Antarctic Peninsula, and Kerguelen). In addition, species delimitation analyses supported a model that considers these four lineages as distinct species. However, as I have discussed in other blog posts (see here and here), genetic population structure does not necessarily coincide with species boundaries. Other data types are needed to validate the delimited species.

Genetic analyses revealed four distinct lineages. But do they represent different species? From: Tyler et al. (2020) Ecology and Evolution.

Morphological Overlap

Next, the researchers performed several statistical analyses on a set of morphological traits. A MANOVA test indicated that “all genetically distinct populations are significantly distinct from each other overall.” However, a closer look at the results of this MANOVA test shows that the p-values are just below the significance threshold of 0.05. For example, the p-value separating the Falklands from Kerguelen is 0.0446. Statistically significant, yes. But is this difference biologically relevant?

My skepticism towards the morphological patterns was reinforced by the output of the linear discriminant analysis where the authors reported that “a small number of specimens occupying positions closer to other lineages.” Moreover, assigning individuals to the genetic lineages using the morphological data resulted in an error rate of 10% (i.e. one individual out of ten was assigned to the wrong lineage). Clearly, the morphological differences are not absolute.

Linear Discriminant Analysis of the morphological data. Circles represent individual specimens with triangles showing the lineage mean. Notice the overlap between SGI (pink) and FALK (blue). Tyler et al. (2020) Ecology and Evolution.

Verdict

So, how convincing is the evidence to recognize four species of Gentoo Penguin? There appears to be some conflict between the genetic and morphometric results. We can recognize four distinct genetic lineages, but they overlap morphologically. And that is a logical finding when you keep in mind that speciation is a gradual process in which different traits evolve at different rates (more details in this blog post). In this case, the Gentoo Penguin populations have become genetically distinct, but the morphological separation might still be under way (or it might stabilize in the current situation). In my opinion, these penguins are in a “taxonomic grey zone”. One could make a case to treat them as subspecies. Or one could argue that the morphological differences are large enough to classify them as distinct species.

An additional argument to recognize four distinct species concerns their conservation status. In the press release, the researchers say that “regarding the four populations as separate species, gives conservationists a better chance of protecting their diversity because if there’s a decline in one of them it will change the threat status as defined by the IUCN Red List”. This is not a biological reason for a taxonomic revision, but a political one. And that is no problem. In light of the current biodiversity crisis it is important to protect as many species as possible. We could have endless academic discussions whether to classify these penguins as species or subspecies, but that won’t safeguard their future. Let’s focus on what matters.

References

Tyler, J., Bonfitto, M. T., Clucas, G. V., Reddy, S., & Younger, J. L. (2020). Morphometric and genetic evidence for four species of gentoo penguin. Ecology and Evolution, 10(24), 13836-13846.

Featured image: Gentoo Penguin (Pygoscelis papua) © Ben Tubby | Wikimedia Commons

Genetic evidence for hybridization between Magellanic and Humboldt penguins

Several genetic markers are useful to identify hybrids and backcrosses.

A few months ago, I published a scoring scheme to assess the reliability of hybrid reports (see this blog post). In short, this scheme is based on three criteria: (1) the observation of a putative hybrid with photographic evidence or a detailed description, (2) thorough morphological analyses in which the putative hybrid is compared with potential parental species, and (3) genetic analyses of the putative hybrid with reference material from potential parental species. To express the varying levels of confidence that each of these criteria provide, I weighted them differently in the final score for a putative hybrid, namely one point for an observation, two for a morphological analysis, and three for a genetic test. The final tally of these three criteria (ranging from 0 to 6 points) will indicate the level of confidence for a particular hybrid combination. I applied this scheme to the tinamous (family Tinamidae), resulting in one well-documented case and three doubtful records that require further investigation.

The goal is to apply this approach to other bird families in order to provide a better overview of the incidence and reliability of bird hybrids. A recent study in the journal Genetica summarized the literature on penguin hybrids and indicated that most hybridization studies were “based solely on morphological or nesting observations, with no genetic confirmation of hybridization.” In the context of the scoring scheme, most cases of penguin hybrids would thus receive a reliability score between 0 and 3 points. Clearly, more genetic studies are needed to determine the incidence of penguin hybrids. And the study in Genetica delivers a nice example for hybrids between Magellanic Penguins (Spheniscus magellanicus) and Humboldt Penguins (Spheniscus humboldti).

Genetic Markers

Eric Hibbets, Katelyn Schumacher and their colleagues focused on six individuals that were sampled at three colonies from the Atlantic Ocean basin (Caleta Valdés, Punta Tombo, and Cabo Dos Bahías). These birds were initially noted down as Magellanic Penguins, but were later identified as putative hybrids based on the presence of mitochondrial variants (of the COI gene) that are characteristic for Humboldt Penguins. The researchers tested this conclusion with three additional genetic markers: a set of six microsatellites, the immune gene DRβ1 and the sex-linked gene CDH1. They sequenced these markers for several reference samples from both species. The analyses revealed that “three of the four markers (COI, microsatellites, and DRß1) were informative because they provided both Magellanic and Humboldt species-specific alleles or haplotypes that could be used to trace species ancestry in hybrid individuals.”

Distribution ranges of Magellanic (S. magellanicus; light gray stripes) and Humboldt (S. humboldti; dark gray) penguins during the breeding season. Reference populations of Magellanic penguins include samples from three colonies in the Atlantic Ocean (Caleta Valdés, Punta Tombo, and Cabo Dos Bahías). From: Hibbets et al. (2020) Genetica

Backcrosses

What about the six putative hybrids? It turned out that four individuals were backcrosses with some degree of genetic introgression from Humboldt Penguins. The remaining two individuals were actually Humboldt penguins instead of hybrids. These results highlight the value of genetic analyses in hybrid detection. Morphological characters or field observations are not always reliable.

Detailed analyses revealed more admixed individuals among the reference samples. Five out of 37 penguins showed some genetic signs of past hybridization events. Interestingly, all five samples come from the Puñihuil colony, which holds a significant number of intermixed nesting sites of Magellanic and Humboldt penguins. More expeditions will probably uncover more penguin hybrids. And not just between Magellanic and Humboldt Penguins. A recent genomic study reported gene flow between several other species (see this blog post for the details). Who know what penguin hybrids will be discovered with genetic data.

Structure analysis of microsatellite and MHC loci of Magellanic and Humboldt penguin samples. Vertical bars represent individuals with assignment probabilities (Q, y-axis) to the Magellanic (gray) and Humboldt (white) populations. The grey and white horizontal bars below the assignment probabilities represent corresponding species-specific mitochondrial haplotypes of those individuals as determined by COI sequences. Asterisks (*) indicate individuals of hybrid origin that were identified by this study. From: Hibbets et al. (2020) Genetica

References

Hibbets, E. M., Schumacher, K. I., Scheppler, H. B., Boersma, P. D., & Bouzat, J. L. (2020). Genetic evidence of hybridization between Magellanic (Sphensicus magellanicus) and Humboldt (Spheniscus humboldti) penguins in the wild. Genetica, 148(5), 215-228.

Featured image: Magellanic penguin (Spheniscus magellanicus) © David | Wikimedia Commons

This paper has been added to the Sphenisciformes page.

Where did all these penguins come from?

Genomic analyses unravel the evolutionary history of these flightless diving birds.

The evolution of penguins (order Sphenisciformes) remains a mystery. Different genetic studies disagree about the evolutionary relationships between particular species, the timing of speciation events and the original distribution of these iconic seabirds. The divergence time of the crown group (all living representatives of the penguins) ranges from 9.9 million years ago (during the Miocene) to 47.6 million years ago (during the Eocene). And the exact area of origin is also a matter of debate: some ornithologists suggest Antarctica with a subsequent expansion into warmer waters, while others point to Australia or New Zealand followed by colonization of the colder Antarctica. One way to settle these debates is to bring out the big guns: genomic data. A recent study in the journal PNAS applied this strategy and analyzed 22 genomes, representing 18 penguin species. Time to find out what they discovered about the evolution of penguins – a word that Benedict Cumberbatch has some difficulty pronouncing (see video below).

From Australia to Antarctica?

Let’s start with the most likely area of origin for penguins. The authors reconstructed the ancestral distributions of the sampled species and identified the coastlines of Australia, New Zealand, and nearby islands as the original range of the ancestor of extant penguins. From there, these birds colonized Antarctica and South America where they diversified into several species. The genomic analyses provide estimates for the timing of these events.

The first branching event led to the establishment of the genus Aptenodytes in the Antarctic, and reconstructions of the ancestral Pygoscelis species indicate that they colonized the Antarctic Peninsula soon after Aptenodytes, pointing to a long history of Antarctic occupation. In the mid-Miocene, the lineage leading to the Spheniscus/Eudyptula ancestor colonized the South American coast, with members of the genera Eudyptes, Eudyptula, Megadyptes, and Spheniscus progressively diversifying and colonizing warmer at-sea environments.

During the cooling event at the transition of the Pliocene and Pleistocene (about 2.5 million years ago), ice shelves expanded across the Southern Ocean, probably reducing connectivity between several penguin populations. This culminated in more speciation events within the genera Pygoscelis, Spheniscus, Eudyptes and Aptenodytes. The figure below provides a nice overview of all these events.

The evolutionary history of penguins based on genomic data. Reconstruction of ancestral distributions (the colored letters on the nodes in the tree) suggest that the ancestor of modern penguins lived in Australia and New Zealand. From: Vianna et al. (2020) PNAS.

Genes Going with the Flow

The phylogenetic tree from the genomic analyses largely agreed with another recent study based on complete mitochondrial genomes (which I also covered on this blog). A few differences between these studies can be explained by hybridization between several penguin species. The researchers write that “some of the main episodes of genomic introgression were detected among erect-crested and the ancestral rockhopper penguin species (17 to 23%), erect-crested and macaroni/royal penguins (25%), and the Galápagos/Humboldt ancestor and Magellanic penguins (11%).” Interestingly, the direction of introgression in some of these species followed the clockwise flow of the Antarctic Circumpolar Current, the ocean current that circles around Antarctica. Individual penguins might have drifted off during foraging trips and were transported to nearby populations where they interbred with another resident species. Quite literally, gene flow.

This study nicely illustrates the power of genomic analyses. There is an enormous treasure of information hidden in the seemingly meaningless strings of A, T, G and C. With clever methods and careful analyses we are now able to find meaning in these DNA sequences and reconstruct the wonderful evolutionary history of life on our planet.

Patterns of introgression between different penguins species and their ancestors. From: Vianna et al. (2020) PNAS.

References

Vianna, J. et al. (2020). Genome-wide analyses reveal drivers of penguin diversification. Proceedings of the National Academy of Sciences, 117(36), 22303-22310.

Featured image: King Penguins (Aptenodytes patagonicus) © Ben Tubby | Wikimedia Commons

This paper has been added to the Sphenisciformes page.