Genetic analyses point to several bouts of gene flow.
The Strait of Taiwan separates the Chinese Bamboo Partridge (Bambusicola thoracicus) from the Taiwan Bamboo Partridge (B. sonorivox). It is easy to imagine that these bird species have been in contact during periods of low sea levels. And indeed, a taxonomic study from 2014 provided evidence for gene flow after their divergence, roughly 1.8 million years ago. However, these genetic analyses – using an isolation-with-migration model – only indicated that gene flow occurred, but not when. A recent paper in the journal Avian Research addressed this knowledge gap using a set of 31 nuclear loci. When did the Chinese and Taiwan Bamboo Partridge exchange genetic material?
Comparing models
The researchers compared several demographic models with different timing of gene flow. The most likely model (with a posterior probability of 0.53) pointed to early gene flow during the first 20 percent of divergence. However, a second model with late gene flow could not be rejected (posterior probability of 0.30). Together, these patterns suggest that the partridges experienced multiple bouts of gene flow. The researchers speculate that “fluctuations in the sea level of the Taiwan Strait during the early late Pleistocene may have led to changes in their distribution alternating between sympatry and allopatry.” This scenario was supported by ecological niche modelling, showing that the ranges of ancestral populations overlapped during the Last Glacial Maximum.
Three different demographic models that could explain the evolutionary history of these partridges. From: Wang et al. (2021).
Merging and diverging
The evolutionary history of the Chinese and the Taiwan Bamboo Partridge was thus shaped by multiple bouts of gene flow. As methods to detect and date gene flow events improve, we can expect to find similar scenarios in other bird species. The glacial cycles of the Pleistocene impacted the distribution of numerous species, regularly giving rise to zones of secondary contact. Many species pairs were probably subjected to cycles of merging and diverging.
These insights can help us to assess the consequences of current climate change. As species distributions change, some previously isolated populations might establish secondary contact and enter a phase of merging. These human-induced hybridization events are both a curse and a blessing. As I wrote in my review on hybridization the Anthropocene: “As humans continue to change the environment and alter species distributions, more anthropogenic hybridization events will definitely occur. This will pose challenges for the conservation of endangered species, but also provide unique opportunities for evolutionary biologists.”
Ecological niche modelling indicated overlap between both partridge species (in green) during the Last Glacial Maximum. From: Wang et al. (2021).
References
Hung, C. M., Hung, H. Y., Yeh, C. F., Fu, Y. Q., Chen, D., Lei, F., … & Li, S. H. (2014). Species delimitation in the Chinese bamboo partridge Bambusicola thoracica (Phasianidae; Aves). Zoologica Scripta, 43(6), 562-575.
Wang, P., Yeh, C., Chang, J., Yao, H., Fu, Y., Yao, C., … & Zhang, Z. (2021). Multilocus phylogeography and ecological niche modeling suggest speciation with gene flow between the two Bamboo Partridges. Avian Research, 12(1), 1-10.
Genetic study provides evidence for four genetic clusters.
Who doesn’t like Atlantic Puffins (Fratercula arctica)? Small black-and-white seabirds with colorful beaks that nest in rabbit-hole-like burrows. It sounds like something out of a fairytale. But these iconic birds do exist and I have had the pleasure of observing one in close proximity. On a holiday in Wales with my father and some friends, we were planning to visit a breeding colony on a nearby island. Due to the bad weather, however, the boat trip was cancelled and we were forced to change our plans. Walking along the Welsh shores, we suddenly discovered a stranded Puffin. This bird was exhausted, but still managed to bite my fathers finger. We brought it (the Puffin, not my fathers finger) to a nearby house where the surprised owner promised to deliver it at an animal shelter. We never knew if he did and what happened to this particular Puffin.
Despite their attractive looks and endangered status, little genetic work has been done on Puffins. Their current taxonomy is largely based on size differences:
F. a. grabae: the smallest subspecies in France, Britain, Ireland and southern Iceland
F. a. arctica: the intermediate subspecies in Norway, Iceland and Canada
F. a. naumanni: the largest subspecies in the high Arctic (e.g., Spitsbergen, Greenland, northern Canada)
A recent study in the journal Communications Biology provided a genomic perspective on this seabird species. Are these subspecies also supported by genetic data?
Four Clusters
Oliver Kersten and his colleagues compared the genetic make-up of 71 birds to detect any population structure. They could delineate four main clusters. The Puffins from Spitsbergen were clearly distinct from the other populations. And there were more subtle differences between birds from Canada, the Isle of May and multiple colonies from Iceland/Norway/Faroe Islands. Interestingly, these four genetic groups do not correspond to the three subspecies described above:
Although the genetically distinct Spitsbergen cluster coincides with the classification of morphologically large puffins in the High Arctic (F. a. naumanni), we observe gene flow from Spitsbergen into Bjørnøya, which has been considered F. a. arctica. Furthermore, the geographic divide between F. a. grabae and F. a. arctica lies farther south than previously thought, with the Faroese puffins being genetically closer to F. a. arctica than to F. a. grabae.
Moreover, the genetic population structure in the nuclear data was not observed in the mitochondrial DNA (mtDNA). The lack of clear population differentiation in mtDNA could be due to recent population expansions (but see also the seabird paradox). More detailed demographic analyses are needed to unravel the evolutionary history of the Atlantic Puffin.
The genomic data pointed to four genetic clusters (see figures c and d). This population structure was not visible in the mitochondrial DNA (figure b), suggesting a recent population expansion. From: Kersten et al. (2021).
Hybrid Population
In the quote above, you could already read that the researchers found “gene flow from Spitsbergen into Bjørnøya”. For readers unfamiliar with islands in the Arctic: Bjørnøya is a small island between Spitsbergen and Norway that houses less than 1000 breeding pairs. Although the Spitsbergen population is clearly differentiated from the other populations, it still contributes to the formation of a hybrid population on Bjørnøya. An interesting case of secondary contact that requires further investigation.
In summary, a genomic exploration of the Atlantic Puffin uncovered four distinct genetic clusters and a region of secondary contact on the small island of Bjørnøya. I wonder where the Welsh Puffin we found on holiday fits in…
References
Kersten, O., Star, B., Leigh, D. M., Anker-Nilssen, T., Strøm, H., Danielsen, J., … & Boessenkool, S. (2021). Complex population structure of the Atlantic puffin revealed by whole genome analyses. Communications Biology, 4(1), 1-12.
Genomic analyses uncover many advanced generation hybrids.
In 1952, Thomas Howell published an extensive monograph on the Yellow-Bellied Sapsucker (Sphyrapicus varius) which then comprised four subspecies: varius, nuchalis, daggetti, and ruber. Based on extensive field observations, he attempted to figure out how often these subspecies hybridize. He came to the following conclusions:
Interbreeding between the races where their ranges meet is variable. It is apparently free between ruber and daggetti, moderate between daggetti and nuchalis and between varius and nuchalis, and rare or absent between ruber and nuchalis and between ruber and varius.
In other words, all subspecies seem to interbreed with one another (albeit at different frequencies). Over time, the taxonomy of these woodpeckers has changed. Ornithologists now recognize three distinct species:
Yellow-Bellied Sapsucker (S. varius)
Red-naped Sapsucker (S. nuchalis)
Red-breasted Sapsucker (S. ruber, with subspecies ruber and daggetti)
These classificatory changes have provided some clarity, but the three species still interbreed in several hybrid zones. While these woodpeckers might give taxonomists a headache, they provide exciting opportunities for evolutionary biologists. Previous studies have already described genetic patterns in the hybrid zones between Red-naped and Red-Breasted Sapsucker, and between Red-breasted and Yellow-bellied Sapsucker. The third combination – Red-naped and Yellow-bellied Sapsucker – remained to be characterized with genetic data. Luckily, a recent study in the Journal of Avian Biologyfilled this knowledge gap.
Hybrid Triangle
Howell (1952) reported moderate hybridization between Red-naped and Yellow-bellied Sapsucker. Is this also reflected in the genetic make-up of these species? Using a set of three traditional markers and a more extensive genomic dataset, Libby Natola and her colleagues explored hybridization dynamics in the Rocky Mountains. The analyses revealed that most birds within the hybrid zone were genetically admixed: 89% based on traditional markers and 52% based on the genomic data. These patterns highlight that traditional markers, such as nuclear genes or microsatellites, tend to overestimate hybridization rates (see also this study on Chukar and Red-legged Partridge). Genomic data provide a more reliable picture.
Next, the researchers performed a more detailed analysis of the admixed individuals. They used “hybrid triangles” to determine the frequency of first-generation hybrids and backcrosses in the hybrid zone. These triangles combine information from a hybrid index (i.e. genetic ancestry of an individual) and the level of heterozygosity to discriminate between different hybrid classes. In general, “pure” individuals are located in the lower corners, while first generation hybrids are at the top. The sides of the triangles indicate backcrosses. These analyses suggested that “the majority of admixed individuals appear to be advanced generation hybrids.”
The “hybrid triangle” shows that most individuals are located on the sides, suggesting that the hybrid zone is comprised of many backcrosses. From: Natola et al. (2021).
Problems with Plumage
Interestingly, the genetic ancestry of these birds was not reflected in their morphology. The researchers used an extensive eight-point system to classify the sapsuckers into different phenotypic classes. However, nineteen birds had genetic ancestry values that did not follow the phenotypic classification. Plumage is thus not a reliable indicator to discriminate between “pure” individuals and several hybrid classes.
And the situation is even more complex than described here. While writing this blog post, another paper on these sapsuckers was published in the journal Molecular Ecology. Apparently, two hybrid zones have collided into a tri-species hybrid zone where all three species interact. The researchers reported that “Surveys of the area […] show that all three species are sympatric, and Genotyping-by-Sequencing identifies hybrids from each species pair and birds with ancestry from all three species.” I will try to cover this study in due time. Stay tuned for another layer of complexity!
References
Billerman, S. M., Cicero, C., Bowie, R. C., & Carling, M. D. (2019). Phenotypic and genetic introgression across a moving woodpecker hybrid zone. Molecular Ecology, 28:1692-1708.
Grossen, C., Seneviratne, S. S., Croll, D. & Irwin, D. E. (2016). Strong reproductive isolation and narrow genomic tracts of differentiation among three woodpecker species in secondary contact. Molecular Ecology 25:4247-4266.
Natola, L., Curtis, A., Hudon, J., & Burg, T. M. (2021). Introgression between Sphyrapicus nuchalis and S. varius sapsuckers in a hybrid zone in west‐central Alberta. Journal of Avian Biology, 52(8).
Natola, L., Seneviratne, S. S., & Irwin, D. (2022). Population genomics of an emergent tri‐species hybrid zone. Molecular Ecology.
Seeing “species as individuals” helps to understand taxonomic disagreements.
More than ten million years. It has been more than ten million years since the Rose-breasted Grosbeak (Pheucticus ludovicianus) and the Scarlet Tanager (Piranga olivacea) diverged. Despite this significant evolutionary gap, these species still managed to produce a hybrid (see this paper for the complete description). This unusual hybrid attracted some media attention – including this piece in National Geographic – prompting some Twitter-accounts to ask the age-old question: what is a species?
Most people still think about the Biological Species Concept, defining species as “a group of organisms that can successfully interbreed and produce fertile offspring.” A very strict application of this species concept will merge any two species that produce the occasional fertile hybrid. If the cross between the Rose-breasted Grosbeak and the Scarlet Tanager turns out to be fertile, should we consider these drastically different birds as members of the same species? No, because the reality is more nuanced and complicated than blindly following the Biological Species Concept.
As I have explained in a previous blog post, most biologists adhere to the General Lineage Concept or the Evolutionary Species Concept. Both of these concepts emphasize the independent evolutionary trajectory of a species. The General Lineage Concept talks about “separately evolving metapopulation lineages”, whereas the Evolutionary Species Concept mentions “the independent evolutionary fate and historical tendencies” of a species. An occasional hybrid – such as the one described above – will not impact the evolutionary trajectory of both species and we should thus not worry about the species status of the Rose-breasted Grosbeak or the Scarlet Tanager. But what about species that regularly hybridize?
Photographs of the hybrid from (a-c) and the putative parental species: Rose-breasted Grosbeak (d) and Scarlet Tanager (e). From: Toews et al. (2022).
Species as Individuals
The situation becomes more complicated when we consider species that regularly interbreed. Think of the Golden-winged Warbler (Vermivora chrysoptera) and the Blue-winged Warbler (V. cyanoptera) in North America, or the Hooded Crow (Corvus [c.] cornix) and the Carion Crow (C. [c.] corone) in Europe. Does the production of hybrids influence the evolutionary trajectories of these lineages? Here, it is important to consider that the origin of species (or speciation) is a gradual process. Before the development of “separately evolving metapopulation lineages”, these lineages might engaged in a complicated and intricate dance of merging and diverging. Due to the continuous nature of the speciation process, it can thus be difficult to establish clear species boundaries.
To understand this issue, I have always found it useful to consider species as individuals (a philosophical perspective introduced by David Hull). An evolutionary lineage can be regarded as an individual that is born (i.e. start of the speciation process) and will die (i.e. extinction). Some individuals will reach adulthood (i.e. become species) while others will not. However, at what point does an individual become an adult? When I look at the children of my nieces, I am confident that they are not adults yet. And when I meet my uncle or aunt at a family gathering, they are clearly adults. But somewhere between the transition from child to adult, there is a gray zone. Just ask any cashier that needs to check the age of her costumers when they buy alcohol.
Seeing species as individuals. But where do you draw the line between child and adult?
Species Criteria
What characteristics would you use to define an adult? You could focus on particular morphological features, such as secondary sexual traits (e.g., the development of a beard in men or breasts in women). Or you could pay attention to particular behaviors that you consider typical for adults. You could even devise a genetic test to measure the length of telomeres. But when you apply these criteria to a group of people – aged 16 to 25, for example – you will probably come to drastically different conclusions depending on the features you focus on. Different traits – whether morphological, behavioral or genetic – will develop at different rates in different people.
The same reasoning applies to species: during the speciation process, different criteria will evolve at different times in the speciation process. The order in which these criteria evolve will be contingent upon the speciation process. In some cases, morphological differences might emerge before genetic differentiation (see for example Redpolls). In other cases, lineages might be genetically distinct despite little morphological change (i.e. cryptic species, such as in the Warbling Vireo). The result is a taxonomic grey zone where different species criteria lead to different conclusions.
This simplified diagram represents a single lineage splitting into two independently evolving lineages (or species). The horizontal lines represent the times at which the lineages acquire different species criteria. This results in a taxonomic grey zone where alternative species criteria come into conflict. Adapted from De Queiroz (2007) Systematic Biology.
Labeling Life
From the perspective of “species as individuals”, it becomes clear where most taxonomic disputes come from. Lineages that are still in the process of speciation – or even subject to reverse speciation, such as American crows and bean geese – end up in a taxonomic grey zone where species criteria come into conflict. Classifying the inhabitants of this grey zone can be extremely difficult because personal preferences of certain taxonomists and political issues (e.g., protection of endangered species) come into play. This will inevitably lead to some man-made “species” that are not strongly supported by biological data. And the ensuing debate can become heated and unfriendly.
Personally, I prefer to acknowledge the fact that some lineages cannot be easily divided into distinct species. It might be better to just refer to them as taxa – not trying to label them as “species” or “subspecies” – and focus on understanding their ecology and evolution. These resulting insights will be more interesting and fulfilling compared to putting an arbitrary label on an individual.
References
Hull, D. L. (1976). Are species really individuals?. Systematic zoology, 25(2), 174-191.
Ottenburghs, J. (2019). Avian species concepts in the light of genomics. In Avian Genomics in Ecology and Evolution (pp. 211-235). Springer, Cham.
Toews, D. P., Rhinehart, T. A., Mulvihill, R., Galen, S., Gosser, S. M., Johnson, T., … & Latta, S. C. (2022). Genetic confirmation of a hybrid between two highly divergent cardinalid species: A rose‐breasted grosbeak (Pheucticus ludovicianus) and a scarlet tanager (Piranga olivacea). Ecology and Evolution, 12(8), e9152.
Avian Hybrids 