Big geological events and a small bird: the evolutionary story of the Rifleman

Can its current distribution be explained by past or recent events?

“Species that appear widespread may in fact be represented by a series of isolated sub-populations with varying demographic and diversity characteristics, and their genetic and phenotypic diversity may therefore be at higher risk of extinction than they first appear.” This statement caught my attention while I was reading a recent Ecology and Evolution paper. In this study, Sarah Withers and her colleagues investigated the population structure of the Rifleman (Acanthisitta chloris) on the North Island of New Zealand. This small bird has limited dispersal capabilities due to its reduced tail and wing morphology. We could thus expect to find many isolated sub-populations of this species across the island. And indeed, the researchers noted that the North Island Rifleman (subspecies granti) is currently limited to a highly fragmented distribution. This observation raises another question: how did this patchy distribution originate? Is it a consequence of past geological changes or recent human-induced impacts?

Three Lineages

To answer this question, the researchers examined the genetic population structure of the Rifleman with two mitochondrial markers (COI and the control region) and a set of twelve microsatellites. The genetic analyses revealed three mitochondrial lineages: an insular population (Little Barrier Island), a southeastern population (Tararua Ranges and Mohi Bush), and a mainland population (the remainder of birds on the island). The microsatellites largely corroborated this division.

But when did these three lineages arise? Based on a mitochondrial molecular clock, it turned out that the insular population split off from the mainland between 1.25 and 2.5 million years ago. This timing corresponds to the rising sea levels during the Pleistocene epoch, resulting in a significant barrier between the mainland and the islands. Surprisingly, the divergence between the southeastern populations and the rest of the mainland was much older, dated to ca. 4.9 million years ago. These results indicate that the current distribution of the Rifleman has been largely shaped by past geological events. Let’s explore these events in more detail below.

A principal coordinates analysis of the microsatellites points to three distinct genetic lineages. From: Withers et al. (2021).

Drawing Lines

The divide between the southeastern and the mainland populations coincides with two biogeographical barriers: the Taupo Line and the Cocknaye’s Line. The first line (Taupo Line) can be explained by the formation of the Manawatu Strait which divided the North Island into a northern and a southern section. The second line (Cocknaye’s Line) follows a mountain range that arose during the Pleistocene, pushing populations into eastern and western regions. Based on their findings, the researchers suggest that “the distribution of genetic diversity within and among North Island Rifleman populations contains the genetic signal of both the Taupo Line and Cockayne’s Line.” Probably, the Rifleman were first divided into northern and southern populations along the Taupo Line. Later on, the southeastern populations were isolated from the rest of the mainland along the Cockayne’s Line. The figure below provides a graphical overview of these events.

The geographical events explaining the current distribution of the Rifleman on North Island. Populations were first divided across the Taupo Line (figure B), followed by further subdivision along the Cockayne’s Line (figure C). From: Withers et al. (2021).

A Special Case

And there you have it: the biogeographical history of the Rifleman. Interestingly, similar patterns have been documented in non-avian taxa, such as insects and plants. But not in birds. The Rifleman seems to be an exception. Indeed, the researchers write that “Rifleman therefore appear to be a remarkable case among birds in that they show the genetic signal of past dispersal barriers on a scale usually seen only in invertebrates and plants.” A bird species with a non-avian history.

References

Withers, S. J., Parsons, S., Hauber, M. E., Kendrick, A., & Lavery, S. D. (2021). Genetic divergence between isolated populations of the North Island New Zealand Rifleman (Acanthisitta chloris granti) implicates ancient biogeographic impacts rather than recent habitat fragmentation. Ecology and Evolution11(11), 5998-6014.

Featured image: Rifleman (Acanthisitta chloris) © Christopher Stephens | Wikimedia Commons

What determines range shifts up and down tropical mountains?

Exploring the impact of different ecological traits.

Some bird species might be on an “escalator to extinction.” As the climate changes and the suitable habitat shifts upslope, the birds have no choice but to move along. At some point, however, the mountain stops and the species might go extinct. This scenario makes intuitive sense, but is obviously too simple. Several other factors play a role in elevational range shifts and not all species will move up the mountain. Indeed, several studies reported that between a third and a fifth of species actually shift downslope.

In a recent Frontiers in Ecology and Evolution paper, Montague Neate-Clegg and his colleagues compiled a dataset of elevational range shifts for 421 bird species. They found that the species tend to move upslope with an average speed of 1.6 meter per year. However, this speed is only an average which does not capture the variation in underlying range shifts. These shifts are influenced by several ecological traits. Let’s head up this mountain of data and explore.

Species Traits

The dataset contained information from eight study sites across the tropics, from Peru to New Guinea. Detailed statistical analyses revealed that “elevational shift rates are associated with species’ traits, particularly body size, dispersal ability and territoriality.” The finding that dispersal ability plays a role in range shifts is not that surprising. Birds that disperse farther are more likely to explore new locations outside of their current distribution. Similarly, the influence of territoriality is also logical. Birds that do not hold territories are more free to move around and colonize new areas. Finally, the relationship between body size and elevational shifts can be explained within the context of life history theory. Small-bodies species shifted their ranges faster. Smaller species tend to have faster life histories, allowing them to rapidly respond to changing environments. Hence, we have three factors – dispersal ability, territoriality, and body size – that make ecological sense.

The analyses showed that body mass and territoriality have an effect on elevational shifts in tropical birds. These graphs illustrate the relationships with mean elevation (A and B), lower limit (C) and upper limit (D) of the distribution. From: Neate-Clegg et al. (2021).

Downhill

As mentioned above, not all bird species move upslope. And indeed, this study also found that a third of the shifts were downslope. What could explain this reversed movement? The authors offer two main ideas: (1) competitor release and (2) tracking of ecological requirements. The first explanation entails the scenario that a competitor goes extinct downhill, allowing another species to extend its distribution into the freely available niche and extend its range downslope. The second explanation is quite intuitive: species move where there is food. If your favorite food source happens to be down the mountain, that is where you will go there.

In the end, this study provides several ecological features to understand the movement of tropical bird species up and down mountains. However, they did not explicitly consider large-scale factors, such as the topography of the landscape and the configuration of the vegetation. A nice opportunity for further research into elevational range shifts. Much remains to be discovered, so I guess it is not all downhill from here.

The percentage of species that shifted downslope. The different shared of grey correspond to mean elevation, upper limit and lower limit. From: Neate-Clegg et al. (2021).

References

Neate-Clegg, M. H., Jones, S. E., Tobias, J. A., Newmark, W. D., & Şekercioǧlu, Ç. H. (2021). Ecological correlates of elevational range shifts in tropical birds. Frontiers in Ecology and Evolution9, 621749.

Featured image: Andean Motmot (Momotus aequatorialis) © Alejandro Bayer Tamayo | Wikimedia Commons

Adaptive introgression between two high-altitude duck species

Genetic analyses suggest exchange of hemoglobin genes.

Last week, Svante Pääbo was awarded the Nobel Prize in Physiology or Medicine “for his discoveries concerning the genomes of extinct hominins and human evolution.” Together with many colleagues, he discovered how Neanderthals and Denisovans have contributed to the evolutionary story of humans. Hybridization appears to have been quite common, leading to genetic exchange among archaic humans and these extinct species. Building on this work, Emilia Huerta-Sánchez and her colleagues documented introgression from Denisovans into Tibetans, allowing the latter to adapt to life at high altitudes. Specifically, the gene EPAS1 – which plays an important role in dealing with low oxygen conditions – was transferred between these ancient hominins. A beautiful example of adaptive introgression.

Similar examples have been reported in animal species that live at high altitudes, such dogs and cattle (see this blog post). However, these cases do not feature humans and thus received less attention from the media. Luckily, there are some science websites – such as this blog – that put the spotlight on some hidden gems in the vast scientific literature on hybridization. Recently, Allie Graham and her colleagues investigated whether adaptive introgression also occurred in two South American duck species: the Speckled Teal (Anas flavirostris) and the Yellow-billed Pintail (A. georgica). Their findings were published in the journal Heredity.

D-statistics

Both duck species are widespread across South America and can be found at high altitudes in the Andes. These mountain populations are thus interesting study systems to understand adaptation to high altitude. Given the examples of adaptive introgression in other high-altitude animals and the high incidence of hybridization in ducks, it seems reasonable to look for evidence of adaptive introgression in these two species. The researchers focused on 31 genes that are involved in the production of hemoglobin and the physiological reaction to low oxygen conditions (i.e. the HIF pathway).

A commonly used test for introgression is the D-statistic, also known as the ABBA-BABA test. The rationale behind this test is quite straightforward: it considers ancestral (‘A’) and derived (‘B’) alleles across the genomes of four taxa. Under the scenario without introgression, two particular allelic patterns ‘ABBA’ and ‘BABA’ should occur equally frequent. An excess of either ABBA or BABA, resulting in a D-statistic that is significantly different from zero, is indicative of gene flow between two taxa. Applying this approach to the two duck species revealed significant D-statistics for the β-globin genes, but not for any of the other genes in the study (i.e. α-globin genes and the HIF pathway).

Calculating the D-statistic indicated an excess of shared alleles between the high-altitude populations of the Yellow-billed Pintail and the Speckled Teal. This pattern can be due to introgression. From: Graham et al. (2021).

Convergent Evolution?

However, a significant D-statistic does not necessarily mean introgression. The same pattern can be the outcome of other evolutionary processes, such as convergent evolution. Perhaps the high-altitude populations of Yellow-billed Pintail and the Speckled Teal independently acquired the same mutations in the β-globin genes? To rule out this explanation, the researchers took a closer look at the genomic region containing these genes. Interestingly, the β-globin gene cluster showed very low genetic differentiation between the high-altitude populations. This reduced differentiation was not limited to the genes, but extended across the whole genomic region. In addition, a phylogenetic network of the β-globin genes revealed a clearly separate cluster of haplotypes that contained introgressed alleles that were identified in a previous study. Together, these patterns indicate that the β-globin gene variants are not the result of parallel mutations, but are identical by descent. Introgression is thus the most likely explanation.

Two lines of evidence suggest that the β-globin gene cluster was introgression. The top figure shows that the genomic region has low genetic differentiation between the high-altitude duck populations. And the lower figure reveals a separate cluster (highlighted in red) with the introgressed genetic variants. Adapted from Graham et al. (2021).

Faster Evolution

All in all, this study provides convincing evidence for introgression of β-globin genes between the two duck species. Moreover, demographic modelling revealed that the genes flowed from Speckled Teal into the Yellow-billed Pintail. This finding allowed the researchers to sketch a possible scenario:

Thus, the yellow-billed pintail received these variants through hybridization and may not have waited for de novo mutations to adapt to the high-altitude environment, but rather acquired beneficial alleles from the standing variation, albeit via another species with a similar genetic background, leading to faster evolution.

Although adaptive introgression seems likely, it remains to be explicitly tested if the exchange of these genes was indeed adaptive. One possible analysis could be performed with the so-called VolcanoFinder. This approach scans the genome for certain genetic patterns that look like volcanos when plotting pairwise genetic differences. In such an analysis, the β-globin gene cluster should be a clearly visible peak, similar to the Andean mountains where these duck species reside.

References

Graham, A. M., Peters, J. L., Wilson, R. E., Muñoz-Fuentes, V., Green, A. J., Dorfsman, D. A., Valqui, T. H., Winker, K. & McCracken, K. G. (2021). Adaptive introgression of the beta-globin cluster in two Andean waterfowl. Heredity127(1), 107-123.

Featured image: Yellow-billed Pintail (Anas georgica) © Brian Ralphs | Wikimedia Commons

Is the Altai Snowcock a hybrid species?

Re-analysis of genetic data questions the hybrid origin of this species.

Hybrid bird species are rare. In my review of hybrid speciation in birds, I listed only seven putative cases with variable levels of supporting evidence. Since the publication of that paper, a few other bird species have been proposed to be of hybrid origin, namely the Salvin’s Prion (Pachyptila salvini) and the Steller’s Eider (Polysticta stelleri). It is, however, difficult to discriminate between hybrid speciation and other evolutionary scenarios, such as incomplete lineage sorting and repeated bouts of introgressive hybridization. Several lines of evidence are needed to confidently conclude that a bird species has a hybrid origin (see for example, the Italian Sparrow [Passer italiae]). That is why I am always very skeptical when someone announces the discovery of a hybrid bird species. As Carl Sagan nicely put it: “extraordinary claims require extraordinary evidence.”

Hybrid Snowcocks

Recently, Li Ding and colleagues proposed that the Altai Snowcock (Tetraogallus altaicus) evolved through ancient hybridization between Tibetan Snowcock (T. tibetanus) and Himalayan Snowcock (T. himalayensis). This conclusion was largely based on a phylogenetic analysis of the mitochondrial D-loop which clustered three hybrid individuals next to the Tibetan Snowcock. Molecular dating analyses suggested that these hybrids shared a common ancestor with the Tibetan Snowcock about 1.8 million years ago. The researchers summarized their conclusions at the end of the paper:

The hybridization between T. tibetanus and T. himalayensis reproduced fertile hybrids during the Quaternary glacial period and repeatedly backcrosses with T. himalayensis during the interglacial period as a result of inheriting many characteristics from T. himalayensis, and glacial dispersal and isolation finally promoted the speciation of T. altaicus.

That is quite a bold statement from a single evolutionary tree. As mentioned above, I am always skeptical about claims of hybrid bird species. And I am not the only one: Martin Päckert was not convinced by the presented evidence and decided to re-analyze the genetic data. His results appeared in the journal Ecology and Evolution.

Phylogenetic Analyses

The hybrid species hypothesis of the Altai Snowcock relies heavily on the phylogenetic position of two mitochondrial haplotypes: H35 and H36. In the original analyses, these haplotypes formed a separate cluster next to the Tibetan Snowcock. However, Päckert could not recover this result. He ran several phylogenetic analyses with different datasets and approaches (I will not bother you with all the phylogenetic details. Interested readers can check the methods section of the paper). Interestingly, only one out of six phylogenetic analyses showed a sister species relationship between haplotypes H35/H36 and the Tibetan Snowcock. All the other analyses indicated that these haplotypes are more closely related to the Himalayan Snowcock. Based on these patterns, Päckert concluded that “Ding et al. (2020) did not discover previously unknown hybrid snowcocks, because haplotypes H35 and H36 just represent another deeply split mitochondrial lineage of the genetically diverse Himalayan Snowcock, T. himalayensis.”

Phylogenetic positions of the haplotypes H35/H36 based on different alignment strategies (with ClustalW on the left and with manual editing on the right) and different analyses (a = Bayesian inference and b = Maximum Likelihood). Most analyses pointed to H35/H36 as most closely related to the Himalayan Snowcock. From: Päckert (2021).

Hypervariable Regions

But what could have caused the faulty position of these haplotypes in the original study? A more detailed analysis of the mitochondrial D-loop identified the culprit, namely the hypervariable region. This section of the gene is – as the name suggests – extremely variable and can lead to errors in the alignment of genetic sequences. When Päckert removed the hypervariable region from the dataset, he uncovered a clear cluster containing the two haplotypes, the Himalayan Snowcock and the Altai Snowcock (confirming the phylogenetic results). There is thus no convincing evidence for a hybrid origin of the Altai Snowcock.

Päckert nicely summarized the lesson from this case study, namely that “results inferred from mitochondrial markers (in particular from those including hypervariable regions) require a thorough quality check.” Moreover, this example illustrates the importance of re-analyzing data and checking bold claims. That is how science progresses.

Phylogenetic networks with and without the hypervariable region clearly show the impact on the position of the haplotypes H35 and H36. From: Päckert (2021).

References

Ding, L., Liao, J., & Liu, N. (2020). The uplift of the Qinghai–Tibet Plateau and glacial oscillations triggered the diversification of Tetraogallus (Galliformes, Phasianidae). Ecology and Evolution, 10(3), 1722-1736.

Päckert, M. (2021). No hybrid snowcocks in the Altai—Hyper‐variable markers can be problematic for phylogenetic inference. Ecology and Evolution11(22), 16354-16364.

Featured image: Tibetan Snowcock © Donald Macauley | Wikimedia Commons