Is Lilian’s Meadowlark a distinct species?

Answering this question with genomic data and acoustic analyses.

The Eastern Meadowlark (Sturnella magna) and Western Meadowlark (S. neglecta) are in secondary contact across North America. It seems plausible that these species hybridize. However, hybridization is difficult to assess because they look alike. To circumvent this issue, Wesley Layton set up a captive breeding program with Eastern and Western Meadowlarks. In 1979, he presented his findings in the journal Nature:

I now report that between 1966 and 1978 I was successful in inducing 25 captive meadowlarks to pair and produce 44 clutches of 158 eggs. Mixed matings among non-hybrids resulted in 90% fertility, not significantly different from the 87% fertility among eggs from pure matings, whereas the fertility of eggs from pairing of hybrids was only 10%. All eggs resulting from pairing the one surviving backcross hybrid were infertile.

These captive crosses clearly indicated that hybrids between Eastern and Western Meadowlark are mostly sterile. This level of reproductive isolation, in combination with differences in songs, contributed to the decision to treat them as separate species.

Although the species-level taxonomy is well-established, it remains unclear how many subspecies there are. The variation in songs and plumage has led to the description of no less than 17 subspecies within the Eastern Meadowlark. More research is needed to bring some clarity in this taxonomic turmoil. A recent study in the journal Ornithology took a first step and focused on two subspecies – S. m. lilianae and S. m. auropectoralis – that are collectively known as Lilian’s Meadowlark.

Genes and Songs

Johanna Beam and her colleagues sequenced the whole genomes of 32 museum specimens: 22 Eastern Meadowlarks (covering 5 subspecies) and 10 Western Meadowlarks. Phylogenetic analyses revealed a surprising pattern. The subspecies S. m. lilianae and S. m. auropectoralis did not belong to the Eastern Meadowlark, but represented a distinct evolutionary lineage. Moreover, there were no signs of gene flow between any of the taxa. Lilian’s Meadowlark might thus be a separate species.

This conclusion was corroborated by acoustic analyses. The researchers studied the song characteristics in 85 recordings of the different taxa. They found “significant differences in starting, minimum, and median frequencies [which] all indicate strongly divergent song between all taxa.” As song might be an important trait in species recognition, these results suggest that Lilian’s Meadowlark is reproductively isolated from Eastern and Western Meadowlark.

Phylogenetic analyses of genomic data indicate that Lilian’s Meadowlark (in green) is a distinct lineage, different from Eastern Meadowlark (in blue) and Western Meadowlark (in brown). From: Beam et al. (2021).

Pluralism

Taken together, Lilian’s Meadowlark seems to be a distinct species. It is genetically separated from Eastern and Western Meadowlark, and it sings a different song. Hence, the researchers suggest to elevate this taxon to species level. This study nicely shows how different lines of evidence – such as genomics and acoustics – can be combined to make solid taxonomic decisions. A pluralistic approach to avian taxonomy is clearly the way to go.

References

Beam, J. K., Funk, E. R., & Taylor, S. A. (2021). Genomic and acoustic differences separate Lilian’s Meadowlark (Sturnella magna lilianae) from Eastern (S. magna) and Western (S. neglecta) meadowlarks. Ornithology, 138(2), ukab004.

Featured image: Eastern Meadowlark (Sturnella magna) © Mike’s Birds | Wikimedia Commons

Applying the Biological Species Concept to Bacteria

Introgression is not limited to Eukaryotes.

Over the years, I have written several blog posts about species concepts (see for example here and here). I argued that most biologists currently follow the General Lineage Concept or the Evolutionary Species Concept, which both regard species as independently evolving lineages. Laypeople are probably most familiar with the Biological Species Concept (or BSC), defining species as “a group of organisms that can successfully interbreed and produce fertile offspring.” However, this concept can be difficult to apply in certain situations, such when populations are geographically isolated and will never meet. Another common criticism is that the BSC cannot be applied to Bacteria because they do not reproduce sexually. You can imagine my surprise when I came across a recent paper in the journal Genome Biology where researchers applied the BSC to Bacteria:

Some bacteria can engage in gene flow via homologous recombination and this observation has led a growing number of researchers to suggest that bacterial species and speciation might be best defined using the same evolutionary theory developed for sexual organisms; the biological species concept (BSC).

Introgression and Recombination

Awa Diop and her colleagues studied more than 30,000 bacterial genomes. First, they classified these genomes into species by using a cut-off value of 94% genetic similarity in a set of core genes. This arbitrary threshold is commonly applied to delineate bacterial “species”. In this study, however, it mainly allowed the researchers to create a set of “species” for further analyses. To determine whether there has been introgression between these different bacterial “species”, the researchers calculated the ratio between homoplasmic (h) and non-homoplasic (m) alleles. A homoplasmic allele is a genetic variant that is not the result of inheritance from parent to offspring (i.e. vertical inheritance). Instead, such an allele can be the outcome of introgression between bacterial species (i.e. horizontal transfer) or convergent evolution (i.e. bacteria that independently acquire the same mutation). Clonal species – that reproduce asexually – are expected to have few homoplasmic alleles and thus a low h/m ratio. Introgression will result in an increased h/m ratio due to the accumulation of homoplasmic alleles.

In addition, introgression will be accompanied by recombination, the exchange of homologous sections of chromosomes. This process leads to the breakdown of linkage between certain alleles – also known as linkage disequilibrium (LD) – across chromosomes. Clonal species don’t engage in recombination and will thus show no reduction in linkage disequilibrium.

The researchers simulated bacterial genomes without gene flow and compared these patterns – in terms of h/m ratio and LD – with the actual data. These analyses revealed that most bacterial “species” showed signs of introgression and only 2.6% were truly clonal. Some kind of sexual reproduction among Bacteria seems to be more common than we expected.

Genomic analyses pointed to high levels of gene flow (or introgression) between bacterial species. From: Diop et al. (2022).

MEPS

Although the level of introgression among bacterial “species” varied extensively (see figure above), it correlated nicely with sequence similarity. The more similar two species are on a genetic level, the higher the level of introgression uncovered in this study. This pattern can be explained by the observation that homologous recombination requires nearly identical stretches of DNA (also known as MEPS, Minimal Efficient Processing Segments). As genomes diverge, the density of these MEPS decreases and recombination becomes less likely. The relationship reported in this study shows a rapid reduction in introgression between 2% and 10% of sequence divergence. This result explains why an arbitrary threshold to define species of about 95% has been so useful in the past. However, introgression occurred between species that were 90% to 98% divergent. The exact threshold for bacterial species boundaries will thus depend on the study system. There is no silver bullet.

The relationship between sequence identify and level of introgression shows a sharp turn at ca. 90% sequence divergence. From: Diop et al. (2022).

From Bacteria to Birds

You might be wondering why I am covering a paper about bacterial species on a blog dedicated to birds. There are two main reasons: (1) I have a broad interest and don’t want to limit myself to literature on avian hybridization, and (2) you can learn a lot from other study systems. In this case, I noticed an interesting parallel between the arbitrary species threshold in birds (ca. 2% divergence in mitochondrial genes) and in Bacteria (ca. 95% divergence in core genes). These thresholds can be useful as a starting point, but are not always reliable (see for example this blog post). Moreover, this study confirmed a growing consensus among biologists studying speciation: introgression is more common than we previously thought. It doesn’t matter whether we are talking about Bacteria or birds.

References

Diop, A., Torrance, E. L., Stott, C. M., & Bobay, L. M. (2022). Gene flow and introgression are pervasive forces shaping the evolution of bacterial species. Genome Biology, 23(1), 1-19.

Featured image: Neisseria gonorrhoeae © Dr. Norman Jacobs | Wikimedia Commons

What caused the decline of the Green Peafowl?

Did past climatic changes or human actions impact this species?

In the current climate of rapid biodiversity loss, it is easy to blame human activities. Land use changes, overexploitation or other anthropogenic factors can certainly contribute to population declines, but in some cases past climatic changes have left their mark. Humans just provided the final push over the edge, hurling the population towards extinction. Disentangling the impact of past climate change and recent human-induced impact is a challenging exercise. Luckily, the methodological toolbox keeps expanding. And these tools are even more powerful when they are combined in an efficient way.

In a recent study, a team of Chinese scientists applied several approaches to understand the downfall of the Green Peafowl (Pavo muticus), an endangered bird species from Southeast Asia. They published their findings in the Proceedings of the Royal Society B.

Demographic Patterns

First, the researchers used genomic data to reconstruct the fluctuations in the population size of the Green Peafowl (you can check out this blog post for more details on the specific method they used, namely a PSMC analysis). This demographic analysis revealed an early population decline between 800,000 and 210,000 years ago, followed by a recovery during the Last Interglacial Period (about 70,000 years ago). After this period, the population started declining again. Unfortunately, it is not possible to determine whether this decline continued into the present day. The results of a PSMC analysis become unreliable in more recent times.

That is why the researchers turned to another approach and sequenced the genomes of five museum samples (from 1956 to 1976). Comparing the genetic make-up of these older specimens with present-day birds pointed to a significant reduction in genetic diversity. It thus seems that the decline in population size from the glacial periods can be extended to the present day.

The demographic PSMC analysis indicated a steady population decline until about 10,000 years ago (left). A comparison between museum specimens and modern samples revealed a significant decrease in genetic diversity, suggesting that the population decline has continued until the present day. From: Dong et al. (2021).

Niche Models

Using genomic data, we have now established that the Green Peafowl has been declining since the last ice age. But we still don’t know whether humans were involved. To answer this question, the researchers took another look at their toolbox. They reconstructed the amount of suitable habitat during the Holocene (less than 10,000 years ago) with Ecological Niche Modelling (ENM). This approach “predicted stationary general range during these periods and imply little impact of climate change.” If we can rule out these climatic changes, it had to be anthropogenic factors. Right?

Not so fast. This type of reasoning would be a black-and-white fallacy (i.e. pretending that there are only two options). To confidently blame human actions, we need more direct evidence. Here, the researchers provided two lines of evidence. First, they reported a negative correlation between human disturbance statistics, such as intensified land use for buildings and agriculture, and the population size of the Green Peafowl. In addition, they referred to written records in Chinese history that described the use of meat and feathers from this bird species.

Several indices of human impact increased over time, such as population size (blue line), area with buildings (orange), cropland (yellow) and grazing land (purple). These variables negative correlate with Green Peafowl population sizes over time. From: Dong et al. (2021).

Shades of Grey

Taken together, it seems reasonable that human factors have played a central role in the decline of the Green Peafowl. Nonetheless, I would argue that the reductions in population size during the Pleistocene might have rendered this species more vulnerable for population decline in more recent times. As mentioned in the previous paragraph, we should not fall victim to a black-and-white fallacy. The world is often comprised of different shades of grey. Safeguarding the future of the Green Peafowl will add some much-needed color.

References

Dong, F., Kuo, H. C., Chen, G. L., Wu, F., Shan, P. F., Wang, J., … & Yang, X. J. (2021). Population genomic, climatic and anthropogenic evidence suggest the role of human forces in endangerment of green peafowl (Pavo muticus). Proceedings of the Royal Society B, 288(1948), 20210073.

Featured image: Green Peafowl (Pavo muticus) © Scaup | Wikimedia Commons

Slow down, please: The evolution of beak morphology in Tanagers

Which evolutionary model best explains the evolution of this bird group?

The early bird gets the worm. This saying not only applies to our everyday life, it can also be relevant for evolution. When a species colonizes a new area, its members might be confronted with numerous vacant ecological niches. Some individuals might adapt to feed on worms, while others prefer grains or fruits. This situation of ecological opportunity sets the stage for rapid diversification and the origin of new species. In other words, an adaptive radiation. From a theoretical point of view, you would expect an initial burst of species diversification followed by slowdown of evolutionary changes as the niches are being filled.

This scenario has been described for island populations, but does it also apply to species that spread across continental landmasses? A recent study in the Biological Journal of the Linnean Society tested this model with such a group of species: the tanagers. About 12 million years ago these birds colonized South America and diversified into more than 300 species with a wide range of beak morphologies. The ideal study system to explore the early burst scenario on a large spatial scale.

Three Models

Nicholas Vinciguerra and Kevin Burns collected data on the beak morphology for 333 out of 377 species of tanagers. Next, they summarized all morphological variation in a few metrics and compared three different evolutionary models to explain the observed variation:

• Brownian Motion (random changes over time)
• Ornstein–Uhlenbeck (evolution towards an optimal value)
• Early Burst (the model described above)

The analyses revealed that the Early Burst model was the best-fitting model. The researchers noted “a rapid burst of bill shape evolution early in the evolutionary history of tanagers followed by a subsequent slowdown toward the present.” This finding supports the scenario that tanagers quickly filled the available morphospace in beak morphology when the ecological opportunities were present. Over time, the available niches filled up and the rate of evolutionary change dropped.

The phylogenetic analyses showed that an increase in new species (blue line) is accompanied by an early burst in beak morphology followed by a slowdown in evolutionary diversification (black lines). From: Vinciguerra & Burns (2021).

Subfamilies

More detailed analyses revealed that the Early Burst model also applied to specific subfamilies, namely the core tanagers (Thraupinae), the highland tanagers (Diglossinae), the warbler tanagers (Poospizinae), the saltators (Saltatorinae) and the honeycreepers and allies (Dacninae). Adaptive radiations nested within a larger adaptive radiation. Similar patterns have been found in Vangas after they colonized Madagascar, but the situation in the tanagers appears more extreme.

However, the accumulation of species and morphological disparity within vangas occurred 23 Mya within an insular system, whereas in tanagers this evolution has occurred on a continental scale in nearly half the amount of time.

Interestingly, the Darwin’s Finches – the textbook example of an adaptive radiation – did not follow the Early Burst model. The lack of this iconic subfamily in the list above can probably be explained by their recent evolutionary origin. The Darwin’s Finches are still in the early stages of an adaptive radiation. If we could wait a few thousands to millions of years, we might see a slowdown in evolutionary rate in these birds.

An overview of the different subfamilies within the tanagers. Five of these groups also showed an Early Burst pattern of diversification in beak morphology.

References

Vinciguerra, N. T., & Burns, K. J. (2021). Species diversification and ecomorphological evolution in the radiation of tanagers (Passeriformes: Thraupidae). Biological Journal of the Linnean Society, 133(3), 920-930.

Featured image: Purple honey creeper (Cyanerpes caeruleus) © Charles J. Sharp | Wikimedia Commons

How different are Mallards and Chinese Spot-billed Ducks on a genetic level?

A recent study detected minor differences on the sex-chromosomes.

Morphologically, Mallards (Anas platyrhynchos) and Chinese Spot-billed Ducks (A. zonorhyncha) are easy to tell apart. First of all, the sexes of the Mallard are drastically different whereas male and female Chinese Spot-billed Ducks look alike. In addition, the Chinese Spot-billed Duck can be recognized by its pale head which is marked by a whitish eyebrow and two black stripes. And it sports a yellow spot on the bill from which it derives its name. Interestingly, these morphological differences do not extend to the genetic level. Analyses of mitochondrial DNA and several nuclear markers could not discriminate between these species.

The observation of clear morphological disparity without genetic divergence is not uncommon in birds. I have covered several cases on this blog, such as redpolls and warblers. A mismatch between morphology and genetics can often be explained by a few differentiated genomic regions that underlie the phenotypic differences. Hence, Irina Kulikova and her colleagues took another look at the genetic make-up of the Mallard and the Chinese Spot-billed Duck. Did they find any genetic differences?

Genetic Outliers

The researchers scanned the genomes of 23 Spot-billed Ducks, 29 Mallards and 3 hybrids. In the end, they obtained more than 3000 genetic loci: 3130 on the autosomes and 194 on the Z-chromosome (i.e. one of the sex-chromosomes in birds). Most of the genetic variants at these loci were shared between the two species, confirming previous work that they are genetically similar. However, genetic differentiation was about 4.5 times higher on the Z-chromosome compared to the autosomes. A more detailed look at this sex-chromosome revealed three loci that were significantly different between Mallard and Chinese Spot-billed Duck. Moreover, these loci popped up when the researchers tested for signatures of divergent selection. There are thus genetic differences between these duck species. We just had to look really hard to find them.

The Z-chromosome is highly differentiated between Mallards and Chinse Spot-billed Ducks. It contains three clear outlier (depicted as triangles) that might underlie the morphological differences. From: Kulikova et al. (2022).

Future Work

Finding the genetic differences between these duck species is only the first step. Now, the researchers want to find out whether these genetic outliers directly contribute to the morphological differences that we observe. We know that genes regulating plumage coloration and bill color often reside on the sex-chromosomes (see this review by Darren Irwin). Mallards and Spot-billed Ducks might be another example. But this hypothesis remains to be tested with more fine-scale genomic analyses. Nonetheless, the researchers are confident that they are on the right track:

Whether these regions are involved in phenotypic differences between the species and sexual dimorphism is the prospect of future work. We believe that whole-genome sequencing along with plumage analyses will shed light on phenotypic evolution and help to identify speciation mechanisms in Mallard and Chinese Spot-billed Duck.

References

Kulikova, I. V., Shedko, S. V., Zhuravlev, Y. N., Lavretsky, P., & Peters, J. L. (2022). Z‐chromosome outliers as diagnostic markers to discriminate Mallard and Chinese Spot‐billed Duck (Anatidae). Zoologica Scripta.

Featured image: Chinese Spot-billed Duck (Anas zonorhyncha) © Alpsdake | Wikimedia Commons