The beak color of the finch

Why do some nestlings in Darwin’s Finches have a yellow beak?

When I write the following sequence – AA, Aa, and aa – you might immediately think of Mendelian genetics. In high school, countless students have learned how to determine the genetic basis of a particular trait from the combination of dominant (A) and recessive (a) genetic variants or alleles. A popular example, apart from Mendel’s peas, concerns eye color: the brown allele is dominant while blue one is recessive. Put the parental combinations in a Punnett square and you can deduce the eye color of their offspring. The reality, however, is more complicated. In humans, eye color is determined by at least 16 genes. Simple Mendelian traits with one dominant and one recessive allele seem to be quite rare. Most traits are polygenic (i.e. influenced by many genes). But from time to time, researchers stumble upon a classic Mendelian case, such as the beak color of nestlings in Darwin’s Finches.

One Gene

In a recent Current Biology study, Erik Enbody and his colleagues unraveled the genetic basis of beak color in young Darwin’s Finches. Previous work showed that nestlings have either pink or yellow beaks. Tracing this trait across a pedigree revealed that it follows basic Mendelian rules: the yellow phenotype is recessive while the pink one is dominant.

Using genomic data for the Common Cactus Finch (Geospiza scandens) and the Medium Ground Finch (Geospiza fortis), the researchers could trace the genetic basis of this trait to a region on chromosome 24. Close inspection of this genomic region pointed to a single nucleotide variant in the gene BCO2. The exact mechanism associated with this genetic variant remains unknown, but might be related to differential gene expression. A less active BCO2-gene results in the deposition of more carotenoid pigments, culminating in a yellow beak.

Nestlings of Darwin’s Finches have either a yellow or a pink beak (Figure A). Genetic analyses of Medium Ground Finch and Common Cactus Finch converged upon the gene BCO2, which resides on chromosome 24 (Figures B and C). A single variant in this gene determines the beak color (Figures D and E). Lower expression of the recessive yellow allele probably results in the yellow phenotype (Figure F). From: Enbody et al. (2021).

Carotenoid Advantages

The different beak color is not restricted to nestlings of the Medium Ground Finch and the Common Cactus Finch. Numerous other species in the Darwin’s Finches radiation show these phenotypes. Plotting this trait on a phylogenetic tree suggests that it arose roughly 0.5 million years ago when the Vegetarian Finch (Platyspiza crassirostris) lineage split from the ground and tree finches. This pattern raises an intriguing question: how was the variation in beak morphology maintained in all these species?

The researchers explored several options. Perhaps heterozygous individuals do better than homozygous ones, ensuring that the recessive allele continues to circulate in the population. There was, however, no evidence for such a heterozygote advantage in the studies species. Or maybe the yellow beak color triggers the parents to bring more food to the nest. This signaling effect sounds plausible, but it is not supported by observations of parental feeding.

In the end, the researchers speculated about possible advantages of increased carotenoid pigments in the yellow beaks of nestlings. First, collecting these pigments in the beak might protect the birds from accumulating toxic products in their body when the carotenoids are broken down. Second, the yellow phenotype could influence maternal investment. Chickens with the yellow skin phenotype (also related to the BCO2-gene) invest more carotenoids in the egg yolk. The same could occur in Darwin’s Finches. Third, variation in carotenoids might alter the color perception of the avian retina (known as spectral tuning) with possible fitness consequences. Plenty of hypotheses to explore, but finding the correct explanation will not be as easy as shelling peas.

The frequency of the yellow allele across the Darwin’s finch radiation. The yellow stars indicate species with the yellow allele, while the black stars point to species without it. The big yellow star corresponds to the likely origin of the allele. From: Enbody et al. (2021).

References

Enbody, E. D., Sprehn, C. G., Abzhanov, A., Bi, H., Dobreva, M. P., Osborne, O. G., Ruben, C.-J., Grant, P.R., Grant, B.R. & Andersson, L. (2021). A multispecies BCO2 beak color polymorphism in the Darwin’s finch radiation. Current Biology, 31(24), 5597-5604.

Featured image: Common Cactus Finch (Geospiza scandens) © Mike’s Birds | 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

Singing a different song: Incipient speciation in the Small Tree Finch

Two island populations are diverging genetically and acoustically.

Speciation – the origin of new species – is one of the best pieces of evidence for evolution. If species were created by some whimsical designer, we would expect to see clear boundaries between them. Instead, we observe populations at different stages of the speciation process. Some populations clearly belong to distinct species while others freely interbreed and cause headaches among taxonomists that try to pigeonhole all this diversity. In addition, the rate at which populations diverge often differs between traits. Genetic changes tend to accumulate over long periods of time whereas behavioral differences can quickly arise (see for example crossbills). Bird song is a beautiful example of a behavioral trait that can kickstart the speciation process. Several species of songbird learn their song from a tutor (mostly the father singing near the nest) and might make mistakes during the learning process. These mistakes can give rise to local dialects and potentially isolate neighboring populations because they do not recognize each others songs. A recent study in the Journal of Evolutionary Biology documented this process in the Small Tree Finch (Camarhynchus parvulus) on the Galapagos Islands.

Genes and Syllables

Diane Colombelli-Négrel and Sonia Kleindorfer focused on two populations of the Small Tree Finch on the islands of Santa Cruz and Floreana. Genetic analyses – based on microsatellites – indicated that these island populations are diverging. The researchers wondered whether these birds have also developed different songs. Studying more than 900 recordings from 112 males revealed 10 syllable types, of which only 4 were shared between the islands. Hence, the Small Tree Finches from Santa Cruz and Floreana are becoming genetically and acoustically different. But do these differences also affect their behavior? When a bird from Santa Cruz ends up on Floreana, will it be able to find a partner and mate?

The Small Tree Finches on Santa Cruz and Floreana differ genetically (left graph) and in the songs that they produce (right graph). Notice that each song is composed of one syllable type. From: Colombelli‐Négrel & Kleindorfer (2021).

Playback

To assess the behavioral response of the birds, the researchers turned to playback experiments. They tested the response of 91 males – 40 on Santa Cruz and 51 on Floreana – to songs from the two islands. These experiments showed that “males had a stronger response to the intruder song from their own geographical area.” This finding suggests that male Small Tree Finches are able to discriminate between local and foreign songs. Whether females are also capable of telling the difference between males from their own island and accidental visitors remains to be tested. If so, it would point to some level of reproductive isolation. Given enough time, we might end up with two distinct species of Small Tree Finch.

Playback experiments showed that male Small Tree Finches responded most to songs from their own island (in black) compared to songs from another island (in grey). From: Colombelli‐Négrel & Kleindorfer (2021).

References

Colombelli‐Négrel, D., & Kleindorfer, S. (2021). Behavioural response to songs between genetically diverged allopatric populations of Darwin’s small tree finch in the Galápagos. Journal of Evolutionary Biology, 34(5), 816-829.

Featured image: Small Tree Finch (Camarhynchus parvulus) © Mike Comber | Wikimedia Commons

Rapid speciation through reshuffling of existing genetic variation

A few genomic regions might contribute to strong pre-mating isolation.

The French biologist François Jacob described the evolutionary process as tinkering. Evolution does not create new organs or functions out of thin air, but instead works with what is available. On the molecular level, the constant influx of (nearly) neutral mutations expands the pool of genetic variation. When the environment suddenly changes, populations might benefit from certain genetic variants that were already present and quickly adapt. For example, this process probably allowed some populations of the Vinous-throated Parrotbill (Sinosuthora webbiana) to rapidly adapt to high altitude conditions on Taiwan. Apart from speedy adaptation, the reshuffling of genetic variants can also fuel the origin of new species. A recent study in the journal Science documents a beautiful example of so-called combinatorial speciation in Sporophila Seedeaters.

Three Genomic Regions

In October 2001, the Ibera Seedeater (S. iberaensis) was first observed within the breeding range of the closely related Tawny-bellied Seedeater (S. hypoxantha). Both species belong to a radiation of southern capuchino seedeaters that originated within the last million years. The perfect study system to understand the genetic underpinnings of rapid speciation. When the researchers compared the genomes of the Ibera Seedeater and the Tawny-bellied Seedeater they noticed that the differences between these species are concentrated in three genomic regions (located on the Z-chromosome and chromosomes 1 and 11). The regions contain several genes involved in plumage coloration, such as TYRP1, OCA2 and HERC1. These patterns suggest that differences in plumage patterns might contribute to reproductive isolation between these species (more on that later).

Interestingly, the genetic variants in these three genomic regions were also found in other seedeater species. The combination in the Ibera Seedeater, however, was unique for this species. The researchers noted that “this result implies that the S. iberaensis phenotype likely arose through the reshuffling of standing genetic variation that already existed within the other southern capuchinos, providing a mechanism for rapid speciation without the long period required for relevant mutations to arise de novo.” An intriguing conclusion that nicely aligns with previous work on this radiation (see for example this blog post).

The Ibera Seedeater (blue) and the Tawny-bellied Seedeater (red) occur in the same region in South America. Comparing their genomes revealed three distinct genomic regions. From: Turbek et al. (2021) Science.

Sexual Selection

In the previous section, I already hinted at a possible role of plumage in reproductive isolation. The researchers provided convincing evidence that this is indeed the case. First, they tested for assortative mating by genotyping several nests of both species. These analyses revealed that all partners belonged to the same species, no hybrids were found (even after accounting for the high rate of extra-pair copulations). Next, the researchers performed playback experiments in which territorial males were presented with different combinations of conspecific and heterospecific song and plumage. These experiments corroborated the patterns of assortative mating: “Each species responded most aggressively to the combination of conspecific song and plumage, exhibited intermediate responses to the treatments with mismatched traits, and largely ignored the heterospecific capuchino traits and those of the control species.”

Together, these analyses point to strong pre-mating isolation between Ibera Seedeater and Tawny-bellied Seedeater. And as explained above, the traits underlying this reproductive isolation probably originated through the reshuffling of already existing genetic variants. Isn’t evolution a wonderful tinkerer?

Playback experiments with mounted specimens showed that birds reacted most strongly to conspecific combinations, suggesting strong pre-mating isolation. From: Turbek et al. (2021).

References

Turbek, S. P., Browne, M., Di Giacomo, A. S., Kopuchian, C., Hochachka, W. M., Estalles, C., … & Campagna, L. (2021). Rapid speciation via the evolution of pre-mating isolation in the Iberá Seedeater. Science, 371(6536), eabc0256.

Featured image: Ibera Seedeater (Sporophila iberaensis) © Hector Bottai | Wikimedia Commons

Genetic evidence for hybrids between Copper Seedeater and Pearly-bellied Seedeater

Or could the genetic patterns be explained by incomplete lineage sorting?

Last year, I published a short paper on tinamou hybrids in which I introduced a scoring scheme to assess the reliability of hybrid records (see this blog post for a summary). In short, I assigned points for different criteria, namely:

• Observation of a putative hybrid with photographic evidence or a detailed description (1 point)
• Thorough morphological analyses in which the putative hybrid is compared with potential parental species (2 points)
• Genetic analyses of the putative hybrid with reference material from potential parental species (3 points)

I decided to put most weight on genetic evidence, because it can be difficult to confidently identify hybrids based on morphology. A specimen with aberrant plumage might be a hybrid, but could also be a color morph. Genetic analyses can often resolve such morphological mysteries. This is nicely illustrated by a recent study in the journal PLoS ONE in which researchers provide some genetic evidence for hybridization between two Sporophila species.

Scoring Plumage Patterns

An extensive survey of Copper Seedeater (Sporophila bouvreuil) and Pearly-bellied Seedeater (Sporophila pileata) across Brazil uncovered a large variation in plumage patterns. The researchers noted that across several Brazilian states “more than one plumage color occurred”, which they explained by age-related changes in coloration. However, the presence of some intermediate plumage patterns points to the possibility of hybrid individuals. To test this hypothesis, Cesar Medolago and his colleagues turned to genetic data by sequencing the mitochondrial gene COI and several microsatellites across a putative contact zone.

First, the researchers scored the plumage coloration of individuals birds from 1 to 4. Individuals were considered as parental species with a score of 1 or 4, and intermediates when scoring 2 or 3. Next, they constructed an evolutionary tree with the mitochondrial data and checked the positions of the intermediate birds in this phylogeny. In general, intermediate birds with score 2 were closer to Pearly-bellied Seedeater, whereas intermediate birds with score 3 were found in a cluster with Copper Seedeater. However, the combination of plumage pattern and mtDNA was not perfect, suggesting that some individuals might represent backcrosses.

Pictures showing the four classes, from pure Pearly-bellied Seedeater (1) through intermediates (2 and 3) to pure Copper Seedeater (4). From: Medolago et al. (2020) PLoS ONE.

Incomplete Lineage Sorting

Based on the microsatellites, the researchers determined the parents at several nests. The analyses revealed all possible parental combinations, including Pearly-bellied Seedeater couples (3 nests), Copper Seedeater couples (3 nests), and mixed couples (6 nests). In four nests, the male was a Pearly-bellied Seedeater and the female a Copper Seedeater. And in two nests, it was the other way around. These findings suggest ongoing hybridization between these two species.

There is, however, an important issue to discuss here. The genetic patterns seem to suggest hybridization, but there is another possibility: incomplete lineage sorting. Imagine a bowl filled with red and blue marbles (representing an ancestral population). As you pour this bowl into two smaller ones (representing the two Seedeater species), you will not get a perfect division between red and blue marbles. A similar process occurred during the speciation process of these birds, some genetic variation present in the ancestral population was incompletely sorted into the two lineages. The sharing of mitochondrial or nuclear variants can thus be explained by incomplete lineage sorting. And indeed, a genomic study on the genus Sporophila suggested that a recent radiation resulted in high levels of incomplete lineage sorting.

The distribution of mitochondrial haplotypes of Pearly-bellied Seedeater (green) and Copper Seedeater (blue) across Brazil. From: Medolago et al. (2020) PLoS ONE.

Conclusions

Nonetheless, the authors from the present study make a convincing case for the possibility of hybridization. They nicely summarized the supporting evidence at the beginning of the discussion:

The main evidence include: i) the widely disjunct distribution of the two species with records of individuals with intermediate plumage patter concentrated near the contact zone; ii) the similar proportion of haplotypes belonging to pileata and bouvreuil clades only in the area embedded within the contact zone, the only of our three areas in which we found the two typical parental plumage patterns together; iii) the presence of males with intermediate plumage in both of the well-supported clades; iv) the decreasing frequencies of males with intermediate plumage and of mtDNA haplotypes that are exclusive of the bouvreuil clade in the direction of the core area of pileata, and v) the fact that intermediate plumage patterns occur frequently in nature only in this pair of southern capuchinos, differently from the other congeners that do reproduce in sympatry.

References

Medolago, C. A., Costa, M. C., Silveira, L. F., & Francisco, M. R. (2020). Hybridization between two recently diverged neotropical passerines: The Pearly-bellied Seedeater Sporophila pileata, and the Copper Seedeater S. bouvreuil (Aves, Passeriformes, Thraupidae). PloS one, 15(3), e0229714.

Featured image: Copper Seedeater (Sporophila bouvreuil) © Dario Sanches | Wikimedia Commons

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 Sciences, 117(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 Evolution, 10(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 Evolution, 154, 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.