Genomic islands of differentiation in seedeaters are mainly the outcome of selective sweeps

New statistical methods point to several soft sweeps that acted on standing genetic variation.

When you compare the genomes of two related species, you will observe a heterogenous distribution of genetic differentiation. Some genomic regions will be very similar, while other are drastically different. In recent years, evolutionary biologists have tried to unravel the evolutionary processes underlying these differentiated genomic regions – also known as “islands of differentiation” (I have covered a few of these studies on birds, including wood-warblers, white-eyes and hummingbirds). Two main explanations are currently under debate. One model suggests that these genomic islands contain loci that contribute to reproductive isolation. When two species interbreed, these barrier loci are expected to be immune to introgression. Hence, they will diverge while the remainder of the genome is homogenized by introgression. Alternatively, local peaks in genetic differentiation might be the result of species-specific selective sweeps. To discriminate between these two explanations, the majority of studies resorted to population genetic summary statistics (e.g., Fst, Dxy, etc.). A recent study in the journal PNAS took a different approach and applied some newly developed statistical methods to this conundrum.

Ancestral Recombination Graph

In 2017, Leonardo Campagna and his colleagues compared the genomes of several Capuchino seedeaters (genus Sporophila). Their analyses uncovered 25 genomic islands of differentiation, containing genes involved in plumage pigmentation. It remained to be determined whether these genomic islands arose because of they contribute to reproductive isolation or because they were the target of species-specific selection. In the new study (led by Hussein Hejase), the researchers revisited these genomic islands with novel statistical tools.

The first method is the ancestral recombination graph (ARG), which describes both the genealogical relationships as well as the changes in those relationships along the genome due to historical recombination events. This approach was recently used to detect introgression between archaic humans, Neanderthals and Denisovans. With regard to the debate of barrier loci vs. selective sweeps, the ARG-approach can be applied to test a particular prediction involving the TMRCA. This abbreviation stands for “time to most recent common ancestor” and concerns the timepoint where two genetic samples find their common ancestor (or in jargon, when they coalesce). Recent selective sweeps are expected to reduce the TMRCA, because the genetic variants that survived the selection process can probably trace their common ancestor back to that event. Based on this reasoning, the researchers developed a statistical test to detect these species-specific selective sweeps. They found that 23 of the 25 genomic islands showed signs of recent selective sweeps in at least one seedeater species.

Example of a selective sweep involving the gene SLC45A2. The selection event results in a reduction in the TMRCA which is visible in the gene tree as a group of samples with short branches (topright figure). The topleft figure shows the situation for a neutral genomic region. From: Hejase et al. (2020) PNAS.

Machine Learning

Next, the researchers turned to machine learning. They trained a machine learning algorithm with simulated data to discriminate between selective sweeps and neutral evolution. Using this approach, they “identified large numbers of apparent species-specific sweeps, many of which coincided with Fst peaks or otherwise occurred nearby genes involved in the regulation of melanogenesis.” One important caveat is that this method is sensitive to biases in the choice of parameters for simulations. The authors have tried to cope with this potential bias by simulating various evolutionary scenarios and validating the outcomes with independent methods. Indeed, the observation that both the ancestral recombination graph and the machine learning analyses point to a preponderance of selective sweeps is certainly a good sign. All in all, it seems likely that most genomic islands of differentiation can be explained by recent, species-specific selective sweeps. However, this conclusion does not rule out the involvement of barrier loci. The authors put it nicely in the discussion.

Thus, both models likely contributed to differentiation in the regulatory sequence of this gene, but at different times and in different species. Notably, the distinction between the two paradigmatic models may not be absolute, since loci that experienced early barriers to gene flow could later undergo selective sweeps, and loci that underwent species-specific sweeps could lead to reduced hybrid fitness resulting in barriers to gene flow.

References

Hejase, H. A., Salman-Minkov, A., Campagna, L., Hubisz, M. J., Lovette, I. J., Gronau, I., & Siepel, A. (2020). Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. Proceedings of the National Academy of Sciences117(48), 30554-30565.

Featured image: Tawny-bellied Seedeater (Sporophila hypoxantha) © Hector Bottai | Wikimedia Commons

What is so special about Darwin’s Finches?

Evolutionary analyses attempt to pinpoint the success of this adaptive radiation.

When I write Galapagos Islands, you might think about Darwin’s Finches. Indeed, this group of birds has become an iconic example of an adaptive radiation on these islands. However, several other bird species reached this archipelago, but never diversified in terms of species numbers or morphology. Think of the Yellow Warbler (Setophaga petechia) or the Little Vermillion Flycatcher (Pyrocephalus nanus). Or what about the Galapagos mockingbirds that are represented by just four species with little morphological differences. The contrast between these species and the more extensive radiation of the Darwin’s Finches raises an intriguing question: what is so special about these finches? A recent study in the journal Ecology and Evolution took the first steps in solving this mystery.

Diversification Rates

Ashley Reaney and his colleagues collected morphological data on 349 species from the Thraupidae family (to which the Darwin’s Finches belong). Next, they ran the Bayesian Analysis of Macroevolutionary Mixtures (BAMM) program to detect changes in evolutionary rates along the phylogeny of this bird group. These analyses revealed that the majority of Thraupidae experienced an early burst in diversification, followed by decreasing rates until the present. There were, however, two exceptions: the Darwin’s Finches and the seedeaters (genus Sporophila). These sections of the evolutionary tree experienced a recent increase in diversification rate – 6 million years ago for the Darwin’s Finches and 21 million years ago for the seedeaters. This dramatic contrast is nicely illustrated in the figure below where the rapid diversification (in red) stands out against the decreasing rates in the overall phylogeny (in blue).

Overall, the Thraupidae phylogeny shows an early burst in diversification, followed by a decreasing rate. Two notable exceptions are the Darwin’s Finches (Co.) and the seedeaters (Sp.). From: Reaney et al. (2020) Ecology and Evolution.

Evolvability

These findings highlight the unique radiation of the Darwin’s Finches, but still leave our original question unanswered: what is so special about these birds? Additional analyses revealed that these finches occupy a far larger area of the beak morphospace compared to the other species (including the seedeaters). In other words, the Darwin’s Finches show a greater variety of beak shapes, allowing them to enter more ecological niches and diversify into several species. And although ecological opportunities and biogeographic factors certainly played a role in the radiation of Darwin’s Finches, the researchers suspect that the unique developmental and genetic features of these birds were equally (or perhaps even more) important.

It is possible that the ancestor of the Darwin’s Finches that arrived on the islands was “already endowed with the genetic propensity to produce the high levels of beak variation needed to explore new dietary niches.” This propensity for diversification – also known as evolvability – concerns several intrinsic factors that allow certain species to rapidly adapt to new environments. These factors might be related to genetics (e.g., certain mutations or gene flow from other populations) or particular developmental programs. Previous research demonstrated that the cranium of Darwin’s Finches is highly modular, allowing different beak traits to evolve independently from one another. Another possibility – which might seem contradictory – involves the integration of the entire cranium through developmental and genetic connections between the different beak traits. The interplay between modular change and integration might explain the impressive evolvability of the Darwin’s Finches.

Darwin’s Finches (in red) occupy a larger section of the beak morphospace compared to all other members of the Thraupidae family. From: Reaney et al. (2020) Ecology and Evolution.

Evo-devo

The researchers conclude that these hypotheses will need to be tested in other adaptive radiations, such as the Hawaiian honeycreepers or the Malagasy vangas. Moreover, future research should focus on the evolution of developmental genetic programs, including those underlying beak morphology (which I covered in this blog post). If we want to understand the diversification of life on our planet, we will have to combine evolutionary analyses with detailed developmental studies. Time for some evo-devo.

References

Reaney, A. M., Bouchenak‐Khelladi, Y., Tobias, J. A., & Abzhanov, A. (2020). Ecological and morphological determinants of evolutionary diversification in Darwin’s finches and their relatives. Ecology and Evolution10(24), 14020-14032.

Featured image: a collage of different Darwin’s Finches (Geospiza magnirostris, Geospiza fortis, Certhidea fusca, Camarhynchus parvulus) © Kiwi Rex | Wikimedia Commons

The taxonomic story of the Stipplethroats

A recent phylogenetic study proposes nine distinct species.

Worldwide, there might be about 50 billion individual wild birds (according to this recent PNAS paper). Taxonomists classified all this diversity in about 10,000 species. Each species has been given a binomial name, consisting of genus and a species name. For example, the house sparrow is also known as Passer domesticus, ever since Linneaus named in 1758. The taxonomic position of the house sparrow has been stable for centuries, but other bird groups have been prone to more changes. Some have been promoted from subspecies to species rank (or the other way around), while others have received different genus names.

A nice example of this taxonomic instability concerns the stipplethroats of South America (currently in the genus Epinecrophylla). These small passerines were considered close relatives of the Myrmotherula antwrens and were classified in the same genus. Genetic studies revealed that the stipplethroats were actually more closely related to the bushbirds of the genera Neoctances and Clytotanctes. This finding resulted in the naming of a new genus for the group: Epinecrophylla. Since taxonomists have pinned down the genus name for the stipplethroats (at least for now), they turned to the species level. A recent study in the journal Molecular Phylogenetics and Evolution proposed to recognize nine distinct species. Let’s meet the stipplethroats!

Genetic Splits

The genus Epinecrophylla contains 21 recognized taxa, but their classification into species and subspecies is still a matter of debate. Using thousands of ultraconserved elements (UCEs), Oscar Johnson and his colleagues reconstructed the phylogenetic relationships between these taxa. At the base of the phylogeny, we find the checker-throated stipplethroat (E. fulviventris), followed by the ornate stipplethroat (E. ornata). The latter one showed deep genetic splits and clear population structure between three subspecies (meridionalis, hoffmannsi and atrogularis), suggesting that there might be multiple species hiding in this section of the phylogeny. However, the situation could be complicated by a potential hybrid zone between atrogularis and meridionalis in southern Peru. More research on the ornate stipplethroat is definitely warranted.

Next, the researchers reported a clear split between the rufous-tailed stipplethroat (E. erythrura) and the white-eyed stipplethroat (Epinecrophylla leucophthalma). These taxa are clearly distinct species, but the classification of subspecies within the white-eyed stipplethroat needs more work (currently containing leucophthalma, phaeonota, sordida and dissita).

Dated phylogenies for the genus Epinecrophylla based on (A) ultraconserved elements and (B) mitogenomes. From: Johnson et al. (2021) Molecular Phylogenetics and Evolution.

Short Branches

The classification of the first four species was rather straightforward, but now we arrive at the “Epinecrophylla haematonota group” which holds eight taxa that have undergone many taxonomic rearrangements. Apart from the position of the brown-bellied stipplethroat (E. gutturalis), the researchers found considerable disagreement between the phylogenetic methods regarding the relationships among the three other main clades in this group (see figure below). The rapid evolution of these birds probably resulted in very short branches between the clades, making it extremely difficult to uncover the exact branching order. More detailed analyses – perhaps using genomic data – might be necessary to solve this phylogenetic knot.

Despite this methodological issue, the researchers could identify four species that diverged at roughly the same time (about 2 to 3 million years ago): the rufous-backed stipplethroat (E. haematonota), the Rio Madeira stipplethroat (E. amazonica), the foothill stipplethroat (E. spodionota) and the Negro stipplethroat (E. pyrrhonota). The classification into genera and species seems to be quite stable, so now taxonomists can dive into the subspecies level.

Different phylogenetic methods lead to different outcomes. From: Johnson et al. (2021) Molecular Phylogenetics and Evolution.

References

Johnson, O., Howard, J. T., & Brumfield, R. T. (2021). Systematics of a Neotropical clade of dead-leaf-foraging antwrens (Aves: Thamnophilidae; Epinecrophylla). Molecular Phylogenetics and Evolution154, 106962.

Featured image: brown-bellied stipplethroat (E. gutturalis) © Hector Bottai | Wikimedia Commons

This paper has been added to the Thraupidae page.

Inferring introgression: Genomic study on hybridizing Darwin’s Finches highlights the importance of field observations

Explaining patterns of introgression required a thorough knowledge of the study system.

Yesterday I assisted in a field course on habitat analysis for ecologists. The students would visit an field site and explore different aspects of the ecosystem. In my section, we would walk through forest plot and try to identify common Dutch tree species. Due to the Corona-measures, most students had learned about these species in an online course, without hands-on experience in the field. And it showed. Some students struggled to identify the species at first. But once they knew which traits to focus on, they managed to identify most species correctly. This experience highlights the importance of fieldwork.

During my postdoc in Sweden, most of my colleagues worked on the genetics of the black-and-white flycatcher system: pied flycatcher (Ficedula hypoleuca) and collared flycatcher (F. albicollis). To my surprise, some colleagues had not seen these species in the wild and seemed uninterested in the natural history of these beautiful birds. They preferred to focus on abstract genetic concepts (which is also interesting). But how can you interpret the genetic data when you don’t know the ecology of the species? A recent paper in the journal Nature Ecology & Evolution illustrates the importance of knowing the ins and outs of your study system.

The pointed beak of the cactus finch (Geospiza scandens) © Mike’s Birds | Wikimedia Commons

 

Geospiza Finches

When I say “Peter and Rosemary Grant”, you will probably say “Darwin’s Finches”. Indeed, the Grants are known for their long-term study of these small passerines on the Galapagos Islands. On the island of Daphne Major, they documented hybridization between medium ground finch (Geospiza fortis) and cactus finch (G. scandens). Their meticulous study revealed that these species are converging morphologically: the long beaks of G. scandens became blunter and the robust beaks of G. fortis became more pointed. The change of beak morphology was greater in G. scandens, suggesting that genes are primarily flowing from G. fortis into G. scandens.

A recent genomic study confirmed this suggestion and went one step further. Sangeet Lamichhaney and his colleagues – including the Grants – compared the patterns of genetic exchange (i.e. introgression) for different parts of the genome. The genetic analyses pointed to extensive introgression of the autosomes (i.e. any chromosome that is not a sex chromosome) and the mitochondrial DNA, but not of the Z-chromosome.

The genetic analyses indicated introgression of the autosomes and of mtDNA, as shown by the position of SLB (G. scandens with blunt beak). On the Z-chromosome, this group of birds clusters with the other G. scandens samples. (Red = G. scandens, Blue = G. fortis). From Lamichhaney et al. (2020) Nature Ecology and Evolution

 

If you would show this result to my genetics-focused colleague in Sweden, she might attribute it to genetic incompatibilities on the sex chromosomes. And indeed, numerous other studies have found strong selection on sex-linked genes, contributing in reproductive isolation (check out this review on sex chromosomes and speciation). In this case, however, the ecology of the species is important. The field observations provided some crucial insights.

All female finches, including hybrid daughters, preferentially mate with males that sing the same song as their fathers’ song: mate choice is based on the imprinting of offspring on the parental morphology and song. The net result of this pattern of mating is the introgression of mtDNA and autosomal genes but few Z chromosomes from G. fortis to G. scandens. Hybrid females from these matings carry a G. scandens Z chromosome and cannot introgress any G. fortis Z chromosome. Hybrid sons, being relatively small, are at a disadvantage in competition with G. scandens males for high-quality territories and mates.

So, the reduced introgression on the Z-chromosome is not due to genetic incompatibilities, but can be explained by the behavior of the birds. The moral of this story: go into the field before you get into the lab.

 

References

Lamichhaney, S., Han, F., Webster, M. T., Grant, B. R., Grant, P. R., & Andersson, L. (2020). Female-biased gene flow between two species of Darwin’s finches. Nature Ecology & Evolution, 1-8.

 

This paper has been added to the Thraupidae page.