Mitochondrial introgression from Red-billed into Black-billed Gulls

But no signs of nuclear introgression (yet).

A few years ago, I wrote a blog post about the genetic population structure of Black-billed Gulls (Chroicocephalus bulleri) in New Zealand. Analyses of the mitochondrial DNA (mtDNA) revealed two major groups, of which one clustered with the Red-billed Gull (C. novaehollandiae scopulinus). This pattern suggests hybridization, but can also be explained by ancestral variation that has not been sorted into both species (i.e. incomplete lineage sorting, see this blog post for a detailed explanation). In other words, these gull species might share mitochondrial variants that were present in their common ancestor.

A recent study in the journal Ibis revisited this conundrum and investigated the genetic make-up of Black-billed and Red-billed Gulls with mitochondrial and nuclear markers. Are we dealing with introgression or incomplete lineage sorting?

Dilution Effect?

When Andrew Given and his colleagues inspected the genetic make-up of 26 Black-billed Gulls, they found six individuals with mtDNA from Red-billed Gulls. In contrast, all Red-billed Gulls possessed mtDNA from their own species. This pattern argues against incomplete lineage sorting where you would expect shared mitochondrial variants in both species. Moreover, the comparison of different demographic models provided statistical support for a model of strict isolation followed by secondary contact. Hybridization is thus the most likely explanation.

Interestingly, there were no signs of introgression in the nuclear DNA (based on six microsatellites). The researchers suggest that extensive backcrossing with Black-billed Gulls has diluted the introgression signature in the nuclear DNA. However, it is also possible that the microsatellites – which only cover a small section of the genome – were not powerful enough to pick up subtle signals of past gene flow (see for example this blog post). A genomic analysis is thus warranted here.

A phylogenetic tree of mitochondrial sequences shows a clear split between both species. However, some Black-billed Gulls carry mtDNA from Red-billed Gulls (highlighted in grey boxes). From: Given et al. (2023).

Desperate Females

The observation that only Black-billed Gulls have acquired foreign mtDNA can tell us something about the behavior of these birds. As you probably know, mtDNA is transferred through the maternal line. Hence, hybridization mainly occurred between female Red-billed Gulls (which supply the mtDNA) and male Black-billed Gulls. This mating pattern could be explained by the female-biased sex ratio in colonies of Red-billed Gulls. Males fledglings and adults show lower survival rates, resulting in an imbalanced sex ratio. Because there are insufficient males for Red-billed Gull females, they turn to Black-billed Gulls. A nice example of Hubbs Principle, which I covered in another blog post.

Despite clear genetic evidence for introgressive hybridization, field observations of hybrids are rare. During more than 50 years of monitoring, the authors found no mixed pairs in the large Kaikoura colony of Red-billed Gulls. And only five cases of hybridization have been reported in literature (see this paper). Nonetheless, you only need a few hybridization events for the exchange of genetic material between species. Or the transfer of mtDNA happened in the distant past. A genomic analysis might provide the answer.

References

Given, A. D., Mills, J. A., Momigliano, P., & Baker, A. J. (2023). Molecular evidence for introgressive hybridization in New Zealand masked gulls. Ibis, 165(1), 248-269.

Featured image: Black-billed Gull (Chroicocephalus bulleri) © Paul Davey | Wikimedia Commons

Do mixed singers lead to introgression in Leaf Warblers?

Looking for gene flow between Sichuan and Gansu Leaf Warbler.

Two little brown birds. Morphologically, it is impossible to tell the difference between the Sichuan Leaf Warbler (Phylloscopus forresti) and the Gansu Leaf Warbler (P. kansuensis). Once they start singing, however, you can easily tell them apart. In addition, genetic analyses revealed that these species diverged about 2.4 million years ago. Clearly, we are dealing with distinct species – despite their morphological similarity.

Later field explorations uncovered sympatric populations in several Chinese provinces (Qiagai, Hezuo and Bola). Interestingly, some individuals in this area produced mixed songs, combining elements from both species. Could this observation be explained by hybridization? Perhaps these leaf warblers are not such “good” species after all.

Two Clusters

In a recent Molecular Biology and Evolution paper, Lei Wu and colleagues sequenced the genomes of 35 individuals: 19 Sichuan Leaf Warblers, 14 Gansu Leaf Warbler and 2 mixed singers. Analyses of their genetic make-up revealed two distinct clusters – corresponding to the two species – with the mixed singers confidently classified as Gansu Leaf Warblers. Moreover, there were no signs of introgression between these clusters.

However, the researchers could not exclude the possibility of past introgression of mitochondrial DNA (mtDNA). Two birds produced typical Gansu Leaf Warbler songs, but carried Sichuan Leaf Warbler mtDNA. More detailed analyses are needed to search for signatures of past introgression.

Genomic analyses uncovered two distinct clusters that correspond to Sichuan and Gansu Leaf Warblers. Mixed singers (indicated with asterisks) turned out to be Gansu Leaf Warblers. From: Wu et al. (2023).

Reproductive Isolation

Based on the genetic results, the researchers suggest that “the pronounced differences in song can […] act as a premating reproductive barrier between these two species.” A logical conclusion, although there is still the possibility that hybrids are sterile or unviable. Again, more research is warranted to figure this out. And while ornithologists work hard to unravel this evolutionary mystery, the birds keep singing their songs. With or without mixing.

References

Wu, L., Dang, J., Tang, L., Cheng, Y., Song, G., Sun, Y., … & Lei, F. (2023). Limited Song Mixing Without Genomic Gene Flow in a Contact Zone Between Two Songbird Species. Molecular Biology and Evolution, 40(3), msad053.

Featured image: Sichuan Leaf Warbler (Phylloscopus forresti) © Craig Brelsford | Shanghai Birding

That’s nuts! Early evolution of the Nutcracker was not driven by co-evolution with pine seeds

Diversification was shaped by biogeographic and climatic factors.

Nutcrackers (genus Nucifraga) are known for caching pine seeds. The birds do not retrieve all the cached seeds, helping the pines in their dispersal. The interdependence of birds and pines sets the stage for co-evolutionary dynamics. Different nutcracker (sub)species seem to have a preference for certain pine species. For example, nutcrackers in Japan forage on Japanese Stone Pine (Pinus pumila) whereas their Siberian cousins prefer Siberian Pine (P. sibirica). As different nutcrackers specialize on particular pine species, they might diverge in beak morphology, setting the stage for ecological speciation. This scenario has been documented in Loxia crossbills (see this blog post) and might thus also apply to nutcrackers.

A recent study in the journal Communications Biology investigated the role of nutcracker-pine mutualism during the evolutionary history of these birds. Surprisingly, the researchers concluded that “local adaptation to pines likely played a minor role.” So, what factors shaped the evolution of nutcrackers?

Three Lineages

Jordi de Raad and his colleagues sequenced the genomes of 31 Eurasian nutcrackers, belonging to the species N. caryocatactes and N. multipunctata. Several genetic analyses pointed to three distinct clusters: (1) northern N. caryocatactes, (2) southern N. caryocatactes, and (3) N. multipunctata. These three lineages originated during the Pleistocene, about two million years ago.

Next, the researchers looked for the morphological differences between these three groups. If co-evolution with pines shaped the evolution of nutcrackers, we would expect clear differences in beak morphology. However, the researchers reported that:

Our analyses show that variation in beak morphology between nutcracker species only contributed marginally to the phenotypic variation between species. Phenotypic diversification of the three main Eurasian nutcracker lineages was primarily driven by variation in flight-related traits (e.g. tail length) as well as in the white extent on the tail feathers, thus suggesting selection pressures unrelated to food resources as a driver for phenotypic diversification.

In other words, mutualism with pines did not significantly influence the evolution of the nutcrackers.

Genetic analyses revealed three distinct lineages of nutcrackers (left figure). Morphological differences between these lineages mainly involved flight-related traits (e.g., tail length and wing length) and the extent of white on the tail. From: de Raad et al. (2022).

Pleistocene

Looking at the divergence times between the three lineages – around two million years ago – suggests that climatic events were the main drivers. The temperature fluctuations during the Pleistocene probably shaped the genetic patterns we observe today. Local adaptation to different pine species might be a more recent event. We know from other studies systems, such as crossbills and Darwin’s Finches, that beak morphology can rapidly evolve under strong selective pressures. More research is needed to unravel the exact series of events that shaped the evolutionary history of the nutcrackers. It will definitely be an interesting story, even though it might be a hard nut to crack.

References

de Raad, J., Päckert, M., Irestedt, M., Janke, A., Kryukov, A. P., Martens, J., Red’kin, Y. A., Sun, Y., Töpfer, T., Schleuning, M., Neuschulz, E. L. & Nilsson, M. A. (2022). Speciation and population divergence in a mutualistic seed dispersing bird. Communications Biology, 5(1), 429.

Featured image: Eurasian Nutcracker (Nucifraga caryocatactes) © Tokumi | Wikimedia Commons

Peregrine Falcons with ‘eye make-up’ might be better hunters

Analyses of photographs support the “solar glare hypothesis”.

Many falcon species have a malar stripe, a distinctive patch of dark feathers below the eye. The exact function of this plumage trait is a matter of debate among ornithologists. It could, for instance, play a role in vision (absorbing excess light in bright conditions) or thermoregulation (helping animals heat up faster in colder environments). A recent study in the journal Biology Letters provided evidence for the “solar glare hypothesis”. According to this explanation, the malar stripe reduces the amount of light that is reflected into the eyes, potentially increasing the hunting efficiency of falcons under bright conditions.

Photographs

Michelle Vrettos and her colleagues inspected pictures of more than 2100 Peregrine Falcons (Falco peregrinus) from across the globe. They measured several characteristics of the malar stripes, which they correlated with local environmental conditions. The analyses revealed a positive relationship between annual solar radiation and four malar stripe measurements (i.e. width, contiguity, prominence and length). In general, Peregrine Falcons with “wider and more prominent malar stripes or overall darker heads were associated with areas of higher solar radiation.” These patterns are in line with the solar glare hypothesis.

However, the authors do indicate that their findings are only correlational (we all know that correlation does not imply causation) and that the statistical effect sizes were relatively small. Hence, these results remain to be confirmed with additional analyses, and perhaps with an experimental approach. Who doesn’t want to apply eye-liner to a Peregrine Falcon?

Different environmental conditions correlated with several malar stripe measurements. Notice that “average solar radiation” is associated with the first four measurements, even though the effect sizes are small. From: Vettos et al. (2021).

Biogeographic Patterns

Although this study supports the solar glare hypothesis, it is always worthwhile to investigate alternative hypotheses. That is why the authors focused on two biogeographical patterns: Gloger’s Rule and Bogert’s Rule.

Gloger’s Rule predicts darker individuals in wetter areas. Proposed explanations for this pattern include camouflage, protection against parasites and dealing with solar radiation (recently reviewed by Delhey 2019). Bogert’s Rule states that darker animals occur in colder regions because dark coloration absorbs more solar radiation and thus ensures proper thermoregulation (as found in gulls, see this blog post).

If the malar stripe in Peregrine Falcons followed these rules, we would expect significant correlations with rainfall (for Gloger’s Rule) or temperature patterns (for Bogert’s Rule). This was, however, not the case. Rejection of these alternative hypotheses does not automatically support the solar glare hypothesis – that reasoning would be a black-and-white fallacy – but it does narrow down the search for the potential function of the malar stripe.

Hybrid Falcons

You might be wondering why I decided to cover this study on the Avian Hybrids website. What is the connection with hybridization? While reading this paper, I remembered a study in Science on hybridization between wolves and domestic dogs. I summarized the findings of this study in an article for the journal Frontiers for Young Minds.

If you watch nature documentaries, you might have noticed that these wolves mostly have gray fur. But perceptive scientists observed that there were some wolves with darker fur. Where did that dark fur come from? The scientists studied the DNA of these wolves and discovered that the dark fur was caused by a particular variant of a gene. Surprisingly, wolves normally do not have this variant of the gene. But dogs do! Further analyses revealed that, in the past, dogs and wolves had pups together. The mixing of these two species led to the exchange of DNA, including the variant gene that gave wolves darker fur. Because of this darker shade, these wolves were better camouflaged in the forest, making them better hunters. The exchange of DNA—or introgression—helped the wolves adapt to their environment.

Perhaps a similar process could occur in falcons? Several falcon species are known to hybridize, both in captivity and in nature (see this page for an overview). Some of these hybrids might develop darker malar stripes, providing them with an advantage when hunting in bright conditions. Time to inspect more photographs!

References

Vrettos, M., Reynolds, C., & Amar, A. (2021). Malar stripe size and prominence in peregrine falcons vary positively with solar radiation: support for the solar glare hypothesis. Biology Letters, 17(6), 20210116.

Featured image: Peregrine Falcon (Falco peregrinus) © Mosharaf hossain ce | Wikimedia Commons

The benefit of “broken” hybrids

Using mismatched hybrids to find plumage genes.

The first sentence of a paper can be very important. It should capture the attention of the reader and spark curiosity. A recent piece in the journal Ecology nailed it: “We study hybrids, in part, because they are broken.” What a great way to start a paper (although you had me at hybrids).

To be clear, the authors were not referring to the reduced fitness of hybrids. Instead, they were writing about recombination, the molecular process that breaks up the genome and reassembles it into novel combinations. This genetic mixing partly explains the mosaic nature of hybrids. They receive genomic regions from both parental species and express them in previously unseen combinations. The disassociation of certain traits in hybrids can help scientists to uncover the genetic basis of these traits. This approach has been used to find “plumage genes” in several species, such as Colaptes woodpeckers and Setophaga warblers.

Black Masks

The Ecology-paper focused on the Golden-winged Warbler (Vermivora chrysoptera) and the Blue-winged Warbler (V. cyanoptera). Hybrids between these species have already provided insights into the genetic basis of a black throat patch. The presence or absence of this trait could be linked to regulatory sequences of the ASIP-gene (see this blog post). However, the black throat patch almost always co-occurs with a black face mask, even in hybrids. It was thus impossible to disentangle the genetic variants that underlie these plumage patterns. Logically, previous researchers assumed that the throat patch and face mask are controlled by the same genetic locus.

Occasionally, however, a special hybrid is born. A bird with a mismatched throat/mask phenotype. In 1934, Kenneth Parkes collected such a rare specimen in Michigan. He speculated that both traits might be controlled by different genetic loci that are tightly linked. Very rarely, recombination would break the linkage between these loci. Unfortunately, he did not have the genetic tools to test this idea. But in June 2020, another mismatched hybrid showed up. And now, we do have the tools to explore its genetic make-up.

Plumage traits of Vermivora warblers and their hybrids. The arrows indicate the co-occurrence of the black throat patch and the black face mask. The hybrid in the picture shows a rare mismatch of these traits. From: Baiz et al. (2021).

Promotors

Marcella Baiz and her colleagues sequenced the genome of this mismatched hybrid. Comparing its genetic make-up with the parental species and other hybrids allowed the researchers to find the genetic basis of these traits. The analyses pointed to a genomic region in front of (or upstream in the genomic jargon) of the ASIP-gene. This locations indicates that it concerns a promotor, the regulatory on-and-off-switch of a gene. Within this promotor region, the researchers found several genetic variants that were associated with the two traits. Close inspection of these variants suggested “the mask promotor is adjacent to the throat promotor upstream of ASIP.”

It thus seems that multiple regulatory sequences determine the deposition of pigments in different plumage patches. Because the mask promotor and the throat promotor are so close together, they are mostly inherited as a single unit. Very rarely, however, they are broken up by recombination, giving rise to a mismatched hybrid.

Next, you only need an observant ornithologist with access to genome sequencing technology.

The genomic region upstream of the ASIP-gene contains the regulatory sequences for the throat and the mask phenotype. From: Baiz et al. (2021).

References

Baiz, M. D., Wood, A. W., & Toews, D. P. (2021). Rare hybrid solves “genetic problem” of linked plumage traits. Ecology, 102(10), e03424.

Featured image: Golden-winged warbler (Vermivora chrysoptera) © Bettina Arrigoni | Wikimedia Commons

The type specimens of the Great Spotted Kiwi are hybrids

They are crosses between Little Spotted Kiwi and Rowi.

During my BSc studies in Biology, I dreamed of discovering a new species. That process would also involve the description of a so-called holotype, a unique specimen or illustration of the novel species. Ideally, the holotype shows the typical characteristics of the newly described species. When no holotype has been designated, taxonomists can also rely on other specimens which are called syntypes. The Great Spotted Kiwi (Apteryx haastii), for example, has two syntypes (CM AV2828 and CM AV2829). These specimens were collected at Okarito – a location on the South Island of New Zealand – during an expedition in 1870-1871.

Genetic analyses of these two syntypes led to an unexpected finding: they are hybrids between the Little Spotted Kiwi (A. owenii) and the Rowi (A. rowi). This discovery emerged from a larger genetic study into kiwi hybridization.

Hybrid Kiwi

Lara Shepherd and her colleagues focused on Okarito because it holds the only remaining natural population of the threatened Rowi. Until 1978, this species co-occurred – and potentially hybridized – with the Little Spotted Kiwi. Given that kiwi can live for more than 50 years, it is possible that some hybrids are still around. And indeed, based on genetic analyses of museum specimens and living birds, the researchers reported “evidence for recurrent hybridization between Rowi and Little Spotted Kiwi over the last 150 years, including one F1 hybrid found in the last 15 years.”

At the moment, however, there are no first-generation hybrids or backcrosses in the Rowi population at Okarito. This suggests that there has been no recent introgression from Little Spotted Kiwi into Rowi. On the one hand, this is good news. High levels of hybridization can lead to genomic extinction when small populations become swamped by another species. On the other hand, hybridization can be beneficial by introducing new genetic variation that allows small populations to adapt to new conditions (although this remains controversial among conservationists who can be obsessed with “genetic purity”).

Genetic population structure of different kiwi species. Notice the “genetic purity” of the Rowi population (in yellow) and the discovery of two recent hybrids (called Jess and AllportsM). The new type specimen for the Greater Spotted Kiwi (A. maxima) has nearly 100% genetic ancestry of this species. It does not seem to be a hybrid specimen. From: Shepherd et al. (2021).

A New Name

Let’s return to the type specimens of the Great Spotted Kiwi. The discovery of their hybrid nature has some interesting implications. A new type specimen for the Great Spotted Kiwi will need to be appointed. Following the International Code of Zoological Nomenclature, the next candidate is a specimen that bears the scientific name Apteryx maxima Sclater and Hochstetter 1861. Genetic analyses of this specimen confirmed that it is not a hybrid but a representative of the present-day Great Spotted Kiwi population (see figure above). Hence, the Great Spotted Kiwi will get a new scientific name.

References

Shepherd, L. D., Tennyson, A. J., Robertson, H. A., Colbourne, R. M., & Ramstad, K. M. (2021). Hybridisation in kiwi (Apteryx; Apterygidae) requires taxonomic revision for the Great Spotted Kiwi. Avian Research, 12(1), 1-13.

Featured image: Little Spotted Kiwi (Apteryx owenii) © Kimberley Collins | Wikimedia Commons

The genetics of range expansion in Anna’s Hummingbird

Do we see local adaptation in the expanding populations?

What happens at the leading edge of a range expansion? Numerous scenarios are possible (see this review for an excellent discussion). As certain individuals explore new territories, they might encounter novel conditions and experience different selective pressures. In some cases, there can be selection for dispersal-associated traits – such as longer wings in insects – accelerating the colonization process.

However, natural selection requires sufficient genetic variation to act upon. A range expansion often involves a series of population bottlenecks as a subset of individuals colonizes new areas. Each bottleneck is accompanied by a reduction in genetic diversity. Here, the level of gene flow between the core population and the leading edge comes into play. High levels of gene flow could counteract the loss of genetic diversity, ensuring enough potential for local adaptation.

Expanding Hummingbirds

A recent paper in the journal Molecular Ecology explored the genetics of range expansion in Anna’s Hummingbird (Calypte anna). This species has experienced a rapid range expansion from their native breeding grounds in California into Canada (in the north) and into New Mexico and Texas (in the east). Previous studies suggested that introduced plants and supplemental feeding partly drove the expansion (similar to Allen’s Hummingbird). These conditions might result in new selective pressures, leading to local adaptation to anthropogenic environments.

Nicole Adams and her colleagues explored the genetic make-up of 241 individuals across the range of Anna’s Hummingbird. They found “no evidence for either local adaptation (comparing native and expanded ranges) or global selection (across all samples).” Hence, there seems to be no clear evidence for local adaptation at the leading edge. This finding could be due to technical limitations of the analyses, which failed to pick up subtle signatures of selection (see also this blog post). However, the researchers offer a biological – and more interesting – explanation: high levels of gene flow.

Genomic tests for selection did not reveal any genetic loci under selection. No genetic variants exceeded the threshold (indicated by the red dotted line). From: Adams et al. (2022).

Gene Flow

Anna’s Hummingbird shows no clear population structure. Additional analyses uncovered low genetic differentiation between the sampled populations. And there appear to be no clear barriers to gene flow. Hence, the researchers concluded that Anna’s Hummingbird represents “one major genetic group”. The high levels of gene flow across its range might prevent local adaptation at the expansion edge.

Moreover, the population expansion might be too recent – starting in the 1940s – to already show genetic signatures of local adaptation. Over time, selection could overcome the homogenizing effects of gene flow, allowing the hummingbirds to thrive in a human-created landscape. The high levels of gene flow certainly provide sufficient genetic variation for selection to work with.

Several genetic analyses revealed little population genetic structure across the range of Anna’s Hummingbird. High levels of gene flow probably prevent population differentiation. From: Adams et al. (2022).

References

Adams, N. E., Bandivadekar, R. R., Battey, C. J., Clark, M. W., Epperly, K., Ruegg, K., Tell, L. A. & Bay, R. A. (2022). Widespread gene flow following range expansion in Anna’s hummingbird. Molecular Ecology.

Featured image: Anna’s Hummingbird (Calypte anna) © Rhododendrites | Wikimedia Commons

Some hybrid parrots don’t care about the boundaries between genera

Recent paper introduces some intergeneric parrot hybrids.

On the Spanish island Tenerife (Canary Islands), Dailos Hernández-Brito and his colleagues observed a peculiar breeding pair. A male Orange-winged Amazon (Amazona amazonica) and a female Scaly-headed Parrot (Pionus maximiliani) produced seven hybrid offspring. The hybrids came in two morphological types: one type was more similar to the male parent, whereas the other resembled the female parent more. The genera that these species belong to – Amazona and Pionus – diverged about 10 million years ago. A long time, but still within the known limits of avian hybridization (maximum divergence time for a bird hybrid is ca. 47 million years of divergence, see this blog post).

In their discussion, the authors noted that “To our knowledge, the only instance recorded in the wild occurred between the last free-living male Spix Macaw Cyanopsitta spixii and a female Blue-winged Macaw Primolius maracana, which after three breeding seasons only produced an unviable embryo.” This statement caught the attention of Andrew Hingston, who presented additional cases of intergeneric hybrids between parrot species in a short Ibis-paper. He indicated that the authors probably missed these cases because they were published in regional Australian journals, such as Australian Bird Watcher and Tasmanian Bird Report.

The two hybrid types between Orange-winged Amazon and Scaly-headed Parrot. From: Hernández‐Brito et al. (2021).

Two Australian Cases

The first case concerns hybridization between Rainbow Lorikeet (Trichoglossus moluccanus) and Musk Lorikeet (Glossopsitta concinna) on Yorke Peninsula in South Australia. Several birds with intermediate phenotypes were photographed. However, it might still concern individuals with aberrant plumage colors. Observations of pairings between Rainbow and Musk Lorikeet provided some evidence for hybridization. Another intergeneric parrot hybrid was reported on eBird: a putative cross between Galah (Eolophus roseicapillus) and Little Corella (Cacatua sanguinea).

Both cases are definitely interesting and possible, but I would nonetheless call for genetic analyses to confirm these hybrids. As James Alfieri and his colleagues wrote in a recent Ecology and Evolution paper: “genetic approaches, such as whole-genome sequencing, remain the gold standard for validating hybridization events.”

Desperate birds

All the intergeneric hybridization events have one thing in common: one of the parental species formed a small population with limited access to conspecific partners. These birds might have settled for a partner of a different species (even belonging to another genus), because they could not find a mate of their own species. This situation is known as Hubb’s Principle. Although I prefer the more explicit term: the “Desperation Hypothesis”. Desperate times call for desperate measures…

References

Hernández‐Brito, D., Tella, J. L., Carrete, M., & Blanco, G. (2021). Successful hybridization between non‐congeneric parrots in a small introduced population. Ibis, 163(3), 1093-1098.

Hingston, A. B. (2022). Hybridization between wild non‐congeneric parrots may be more common than previously thought. Ibis, 164(2): 603-605.

Featured image: Rainbow Lorikeet (Trichoglossus moluccanus) © Andrew Mercer | Wikimedia Commons

Surprisingly high genome-wide diversity in the California Condor

A genetic legacy from a prehistoric abundance.

In 1987, the California Condor (Gymnogyps californianus) was extinct in the wild. All the remaining wild individuals were captured and entered into an extensive captive breeding program. Beginning in 1991, the condors were reintroduced into the wild. At the moment that I write this blog post, the total population is estimated at 557 birds, of which 343 live in the wild (you can follow the status of the population here).

Having been on the brink of extinction, you might expect very low genetic diversity in the California Condor (see for example this blog post). Surprisingly, that is not the case. A recent study in the journal Current Biology reported that “[f]or a species that was briefly extinct in the wild, the California condor has unexpectedly high genome-wide diversity.” How can we explain this counterintuitive pattern?

Demographic Analyses

Jacqueline Robinson and her colleagues generated a high-quality genome of the California Condor. The largely contiguous genome sequence allowed them to explore the genetic make-up of this vulture in great detail. High levels of inbreeding – even before its near extinction – left a clear genetic signature as so-called “runs of homozygosity” (ROHs). These runs are stretches of DNA with no genetic variation. More than 20% of the Californian Condor genome contained these deserts of low genetic diversity (compared to only 5.7% in the Andean Condor and 4.24% in the Turkey Vulture).

Despite the prevalence of these ROHs, the genome-wide diversity was unexpectedly high (as I already mentioned above). This pattern can be explained by the demographic history of the Californian Condor. Reconstructing the past effective population size of this species revealed that it used to be very abundant (see this blog post for more information about the method). The researchers noted that “California Condors were more abundant than either Andean Condors or Turkey Vultures for much of the Pleistocene” (although this statement has been questioned, see here and here).

Historical effective population sizes of Californian Condor (brown), Andean Condor (blue) and Turkey Vulture (green). From: Robinson et al. (2021).

History Matters

The high genome-wide diversity in the California Condor is thus a legacy from its prehistoric abundance. This finding highlights the importance of taking into account the evolutionary history of a species. Present-day patterns can often be explained by past events. As John Michael Crichton (the author of Jurassic Park) nicely put it: “If you don’t know history, you don’t know anything. You are a leaf that doesn’t know it is part of a tree.”

References

Robinson, J. A., Bowie, R. C., Dudchenko, O., Aiden, E. L., Hendrickson, S. L., Steiner, C. C., Ryder, O. A., Mindell, D. P. & Wall, J. D. (2021). Genome-wide diversity in the California condor tracks its prehistoric abundance and decline. Current Biology, 31(13), 2939-2946.

Featured image: California Condor (Gymnogyps californianus) © Scott Frier Nikon | Wikimedia Commons

Dating with different techniques: Consilience of divergence times between Bean Goose species

Several methods suggest that Taiga and Tundra Bean Goose diverged about 2.5 million years ago.

One of the strongest arguments for evolution is consilience, the principle that evidence from independent, unrelated sources converges upon the same conclusions. Numerous lines of evidence, from genetic analyses and comparative morphology to biogeography and embryology, all point to the same unescapable conclusion: life on Earth evolved over billions of years. Doubting evolution would just be silly.

The principle of consilience can also be applied to smaller questions. In my own work on the evolution of geese, I uncovered a nice example of consilience: the divergence between Taiga Bean Goose (Anser fabalis) and Tundra Bean Goose (A. serrirostris). Using different dating techniques, I always converged upon the same answer: these species diverged around 2.5 million years ago.

mtDNA vs. Genomics

Before we delve into my goose work, we start with a study in the Journal of Evolutionary Biology. In 2000, Minna Ruokonen and her colleagues compared about 1000 base pairs of the mitochondrial DNA for seven goose species. Although they only included a sample of the Tundra Bean Goose (and not the Taiga Bean Goose), we can still compare this species with other closely related goose species, such as the Pink-footed Goose (A. brachyrhynchus). Based on the level of genetic divergence in the mtDNA, the researchers provided “a rough estimate for the timing of speciation events of Anser species […] within approximately 2–2.5 million years.”

More than 15 years later, during my PhD at Wageningen University, I used genomic data to unravel the evolutionary history of these goose species. After constructing a phylogenetic tree (based on 6,630,626 base pairs), I ran a molecular clock analysis with the software MCMCtree. First, I estimated a mean substitution rate based on previous studies. Next, the split between the two goose genera – Anser and Branta – was constrained between 4 and 20 million years, the time period for which we have reliable goose fossils. And finally, the MCMCtree analyses were run multiple times to check for convergence of the results. Using this approach, the divergence between Taiga Bean Goose and Tundra Bean Goose was estimated ca. 2.5 million years ago. Very similar to the mitochondrial result by Minna Ruokonen and her colleagues.

Genomic data suggested that the Taiga Bean Goose (in green) and the Tundra Bean Goose (in orange) diverged around 2.5 million years ago. From: Ottenburghs et al. (2016).

Demographic Models

So, now we have two independent lines of evidence for the divergence time between Taiga Bean Goose and Tundra Bean Goose. But it gets even better. During my postdoc at Uppsala University, I focused on the evolution of these two species (and later adding the Pink-footed Goose to the mix). To understand their evolutionary dynamics, I opted for a demographic modelling approach with genomic data. Using the software package DADI, I compared different demographic scenarios, ranging from strict isolation to secondary contact with asymmetrical gene flow.

DADI simulates the change in allele frequencies using a diffusion equation, similar to gas molecules moving through a room. Depending on the interplay of genetic drift, selection and migration, genetic variants spread through a population at different speeds. The end result can be visualized in a square with different populations on the horizontal and vertical axes (in my case, the two Bean Goose species). Genetic variants that are unique for one of the species can be found in the lower left corner, whereas variants shared by both species are found in the top right corner. Gene flow between the populations mixes things up. Different demographic models lead to different squares which can be compared to the actual data.

My genomic analyses pointed to a scenario of allopatric divergence (about 2.5 million years ago) followed by recent secondary contact (about 60,000 years ago). Another independent line of evidence for the divergence time between Taiga Bean Goose and Tundra Bean Goose.

DADI uses a diffusion equation to simulate how genetic variants spread through a population. The result can be visualized in a square and compared with the actual data. For the Bean Geese, the close match between the data and the model suggested a scenario of allopatric divergence with secondary contact. From: Ottenburghs et al. (2020).

Consilience

And there you have it. Three independent analyses that all converge upon the same conclusion. It does not matter if you use a simple calculation based on mitochondrial divergence, a molecular clock calibrated with fossils, or a demographic model using diffusion equations. The conclusion is always the same: Taiga Bean Goose and Tundra Bean Goose diverged ca. 2.5 million years ago. Now, that is consilience.

References

Ottenburghs, J., Megens, H. J., Kraus, R. H., Madsen, O., van Hooft, P., van Wieren, S. E., Crooijmans, R. P. M. A., Ydenberg, R. C., Groenen, M. A. M. & Prins, H. H. T. (2016). A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese. Molecular Phylogenetics and Evolution, 101, 303-313.

Ottenburghs, J., Honka, J., Müskens, G. J., & Ellegren, H. (2020). Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation. Heredity, 125(1-2), 73-84.

Ruokonen, M., Kvist, L., & Lumme, J. (2000). Close relatedness between mitochondrial DNA from seven Anser goose species. Journal of Evolutionary Biology, 13(3), 532-540.

Featured image: Taiga Bean Goose (Anser fabalis) © Marton Berntsen | Wikimedia Commons