The constrained evolution of a hybrid species, the Italian Sparrow

Unraveling the complex interplay between standing genetic variation and genetic incompatibilities.

The genome of a hybrid species is a mosaic of its parental species. In the case of the Italian Sparrow (Passer italiae), it is a mixture of the genetic material from the Spanish Sparrow (P. hispaniolensis) and the House Sparrow (P. domesticus). Combining the gene pools of two species might provide hybrid species with an unprecedented level of evolvability, allowing them to quickly adapt to new environments. There is, however, an important catch: genetic incompatibilities. The parental species have diverged over time and some genetic combinations might not work in a hybrid. Such incompatible variants can result in significant evolutionary constraints. In a previous blog post, I illustrated this situation with dealing cards. Each card can be seen as a specific genomic region. Black cards represent the House Sparrow and red cards the Spanish Sparrow. Some genomic regions might come exclusively from one parent. For example, you will always receive a black queen, but never a red one. There are thus some constraints on the formation of hybrid genomes: not all combinations are possible. A recent study in the journal Molecular Ecology explored whether such constraints have influenced the evolution of the Italian Sparrow.

Genetic Variation

Angélica Cuevas and her colleagues took a closer look at the genomes of 131 Italian Sparrows and uncovered moderate genetic differentiation between eight populations. Interestingly, the genetic differences between these Italian Sparrow populations were mainly found in genomic regions that are not divergent between the House Sparrow and Spanish Sparrow. This observation suggests that not all parental variation is available for the Italian Sparrow. Some (divergent) genetic variants might be incompatible and will be purged from the hybrid population.

Do these incompatibilities hamper the evolution of the Italian Sparrow? Although they might prevent certain variants from reaching this hybrid species, there is still plenty of genetic variation available for adaptation. In fact, the analyses provided no evidence for novel variation (i.e. recent mutations in the Italian Sparrow) being important in local adaptation. Instead, the researchers write that “Standing genetic variation inherited from the parental species is a likely explanation for much of the genomic variation in the hybrid species, and some of the variation may be involved in subsequent local adaptation.” Indeed, detailed genomic analyses revealed several genomic regions under selection, containing some interesting candidate genes involved in the development of beak morphology.

Genomic analyses uncovered moderate population structure in the Italian Sparrow. The genetic variants underlying this differentiation were not divergent between the parental species, suggesting some evolutionary constraints. From: Cuevas et al. (2021) Molecular Ecology.

Delicate Balance

This study nicely illustrates the benefits and downsides of hybrid genomes. On the one hand, genetic variation from both parental species provides the opportunity for rapid adaptation. On the other hand, genetic incompatibilities prevent the formation of certain genomic combinations and can thus constrain evolutionary changes. In the end, some hybrid species will manage to find a viable balance between these opposing forces, allowing them to thrive in novel environments that are unavailable to their parental species. As Anna Runemark, Mario Vallejo-Marin, and Joana Meier wrote in a recent review: “Hybrid genomes are important components of biodiversity and hybrid origin may spur adaptation. Future investigations into the properties of hybrid genomes will improve our understanding of the potential of hybridization to produce novel adaptive variation.” The Italian Sparrow will certainly continue to contribute to our quest to understand the evolution of hybrid genomes.


Cuevas, A., Ravinet, M., Sætre, G. P., & Eroukhmanoff, F. (2021). Intraspecific genomic variation and local adaptation in a young hybrid species. Molecular Ecology30(3), 791-809.

Featured image: Italian Sparrow (Passer italiae) © Omar Bariffi | Flickr

Unraveling the evolutionary history of the Manakins

Different methods largely converge on the same species tree.

Constructing a phylogeny from genomic data is a challenging exercise. Some researchers have proposed a concatenation approach where you combine all genes into one long sequence and analyze them as one huge gene. This straightforward strategy has the major limitation that it assumes all genes share the same evolutionary history. This is mostly not the case: different genes tend to tell different evolutionary stories. So, how can you extract the “true” phylogeny from this forest of discordant gene trees. Here, the multispecies coalescent (MSC) can be useful. This statistical framework uses a set of discordant gene trees to estimate the species tree, while taking into account their diverse evolutionary trajectories (often caused by incomplete lineage sorting). Although there has been intense debate on this method, it does seem to be a reliable way to reconstruct species trees. A good strategy is to apply multiple methods and try to understand any incongruent results that pop up. In my own research on the evolution of geese, for example, I applied both concatenation and multispecies coalescent approaches. Both methods converged on the same species tree, suggesting that it reflects the main evolutionary history of these birds. Recently, a study in the journal Molecular Phylogenetics and Evolution used a variety of methods to unravel the phylogenetic relationships of manakins (family Pipridae). Let’s see if they succeeded.

Many Methods

Rafael Leite and his colleagues sequenced two types of molecular markers for several manakin species: ultraconserved elements (UCEs) and exons. UCEs are genomic sequences that are highly conserved across vertebrates and can thus be easily sequenced across a wide range of species. Their flanking regions are more variable and can be used for phylogenetic analyses (see for example this study on honeyeaters). Exons are the expressed sections of gene sequences and can be obtained with specific target capture methods. These two types of molecular markers were subsequently analyzed with both concatenation and multispecies coalescent approaches.

The researchers used the UCE data to create two datasets: one with at least 75% of the species sampled (75% UCE) and one with at least 95% of the species sampled (95% UCE). Next, they performed the following phylogenetic analyses: concatenated analyses on three datasets (75% UCE, 95% UCE and exons) and multispecies coalescent on two datasets (75% UCE and 95% UCE). For the latter analyses, they relied on two approaches: ASTRAL (which uses the gene trees as input) and SVDquartets (which uses the sequence data as input).

Phylogenetic tree of the manakins (family Pipridae) based on Maximum Likelihood analyses of the UCE concatenated datasets. The numbers in the boxes indicate support values for the 75% UCE and 95% UCE datasets. From: Leite et al. (2021) Molecular Phylogenetics and Evolution.

Non-monophyletic Clades

I will not bother you with a detailed description of all the resulting phylogenies. The researchers noted that their results “were largely congruent across analyses, and led to a robust hypothesis about the phylogenetic relationships of manakins.” In line with previous molecular studies, the analyses pointed to an early split between the sexually monomorphic genera Neopelma and Tyranneutus (group A, subfamily Neopelminae), and the dichromatic “core” manakins (group B, subfamily Piprinae). In addition, the results suggest sub-clades B1 (Ilicura, Masius, Corapipo, Chiroxiphia and Antilophia) and B2 (Xenopipo, Chloropipo, Cryptopipo, Lepidothrix, Heterocercus, Manacus, Pipra, Machaeropterus, Pseudopipra and Ceratopipra) within the Piprinae.

Most genera turned out to be monophyletic, but there are some notable exceptions. First, several species of the genus Tyranneutus – namely the Tiny Tyrant-manakin (T. virescens) and the Dwarf Tyrant-manakin (T. stolzmanni) – are nested with the genus Neopelma. Second, the analyses indicated that two species of the genus Antilophia – the Helmeted Manakin (A. galeata) and the Araripe Manakin (A. bokermanni) – cluster within the genus Chiroxiphia. Moreover, different methods pointed to different phylogenetic relationships between the members of these genera (although Antilophia was always nested within Chiroxiphia). More work is needed here to sort out the details, but a taxonomic revision seems warranted.

Different methods resulted in different topologies for the genera Antilophia and Chiroxiphia. From: Leite et al. (2021) Molecular Phylogenetics and Evolution.

Future Work

Despite some phylogenetic conflicts between the methods and a few clades with low statistical support, this study generated a reliable backbone for the manakin phylogeny. This phylogenetic framework can now be applied to macroevolutionary questions to better understand the evolution of the unique behaviors and morphological variation of these beautiful birds.


Leite, R. N., Kimball, R. T., Braun, E. L., Derryberry, E. P., Hosner, P. A., Derryberry, G. E., Anciaes, M., McKay, J. S., Aleixo, A., Ribas, C. C., Brumfield, R. T. & Cracraft, J. (2021). Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness. Molecular Phylogenetics and Evolution155, 107013.

Featured image: Graphical abstract from the study.

Swapping pigmentation genes across the Parulidae phylogeny

Genomic analyses reveal repeated exchange of pigmentation genes among these warblers.

The bird family Parulidae is known for its diversity in plumage patterns, primarily related to the pigments melanin (brown and black colors) and carotenoids (yellow, red and orange colors). Several studies have unraveled the genetic basis of these color differences, usually taking advantage of natural hybrids. Because genetic material gets shuffled around in hybrids, it can be easier to pinpoint particular genomic regions and identify candidate genes for further research. Most of these studies focused on hybridization between two species, such as the hybrid zone between Townsend’s Warbler (Setophaga townsendi) and Hermit Warbler (S. occidentalis). In a recent Current Biology study, Marcella Baiz and her colleagues took a broader perspective and compared the genomes of all 34 species in the genus Setophaga.

Gene Trees

Probing the genomes of these warblers revealed several divergent genomic regions that were shared by multiple species pairs. Some smaller regions contained the pigmentation genes ASIP (agouti signaling protein) and BCO2 (beta-carotene oxygenase 2). These genes also popped up in other studies on plumage coloration (see for example here and here) and are thus excellent candidates for more detailed analyses. Because different species have independently evolved similar plumage patterns, it is possible that these genes have been exchanged across the phylogeny of the Parulidae. To unravel the evolution of these genes, the researchers constructed gene trees for ASIP and BCO2, and compared these with the species tree.

The gene tree of ASIP was largely concordant with the expected phylogenetic relationships, suggesting that it has not been exchanged between species. The convergent evolution of black plumage patterns (in which ASIP is involved) might thus be due to repeated mutations. The situation for BCO2 is drastically different. Its gene tree deviated from the species tree, revealing several instances of introgression between distantly related species. These patterns were confirmed with the D-statistic, a commonly used test to detect introgression. The BCO2-gene has been exchanged between the Magnolia Warbler (S. magnolia) and the Yellow Warbler (S. petechia), and there was probably an introgression event involving the ancestor of the Prairie Warbler (S. discolor) and the Vitelline Warbler (S. vitellina).

The discordance between the species tree (left) and the BCO2 gene tree (right) point to repeated introgression of this gene. From: Baiz et al. (2021) Current Biology.

Tip of the Iceberg

These patterns show how the plumage patterns in the Parulidae evolved through the interplay of repeated mutations in some genes and extensive introgression of other genes. This study focused on just two genes (ASIP and BCO2), but many more genomic regions and candidate genes are waiting to be studied in more detail. The authors wrote that the parulid warblers have a “rich legacy of study, including cornerstones of community ecology and phylogenetic diversification”. I am confident that this bird family will continue to be a focal point of much more scientific research.


Baiz, M. D., Wood, A. W., Brelsford, A., Lovette, I. J., & Toews, D. P. (2021). Pigmentation genes show evidence of repeated divergence and multiple bouts of introgression in Setophaga warblers. Current Biology31(3), 643-649.

Featured image: Magnolia Warbler (Setophaga magnolia) © Cephas | Wikimedia Commons

How the Pleistocene glacial cycles drove the evolution of Arctic shorebirds

An extensive study of 69 species highlights the role of glacial and interglacial periods.

During my PhD on the evolution of geese (see this blog post for a summary), I came across the work of Pieter Ploeger. In 1968, he published an extensive overview on the distribution of arctic ducks and geese during the last ice age. Using a diverse set of data, he tried to pinpoint the areas where these birds resided during the last glacial maximum. The results of this exercise made intuitive sense, but were difficult to test at the time. The development of Species Distribution Models (SDMs) has allowed researchers to reconstruct the past distribution of species and test biogeographical hypotheses, such as the ones put forward by Ploeger. A recent study in the Journal of Biogeography used this approach to investigate how the glacial cycles during the Pleistocene affected the distribution and consequent evolution of arctic shorebirds.

Four Scenarios

Angel Arcones and his colleagues focused on 69 shorebird species and tested four scenarios that could explain the current morphological and genetic patterns. The first scenario (scenario A) assumes that the observed variation might predate the Pleistocene and the glacial cycles had thus no effect on the distribution of these species. The other three scenarios do entail an effect of the Pleistocene glacial cycles, but differ in timing. Populations could become isolated during the warmer interglacial periods (scenario B), the colder glacial periods (scenario C), or both (scenario D). To discriminate between these possibilities, the researchers used Species Distribution Models to determine the distribution of these shorebirds during the last glacial maximum (about 20,000 years ago).

The researchers made a distinction between species that show little morphological or genetic variation (i.e. monotypic species) and species that do. The results revealed that most of the monotypic species (over 65%) did not experience range fragmentation during the last glacial maximum. The more variable species, on the other hand, did show signatures of range fragmentation (62%). The most likely scenarios underlying these fragmentated distributions were roughly equally represented. These patterns confirm the idea that the Pleistocene glacial patterns have shaped the current morphological and genetic patterns in several arctic-nesting species.

The percentage of distributions of the monotypic shorebird species (orange) and species with subspecies (blue) that are explained by the four scenarios. From: Arcones et al. (2021) Journal of Biogeography.

Palearctic and Nearctic

A more detailed look at the results showed that the patterns differ between regions. In Beringia and the eastern Palearctic, climatic conditions were more stable and this area remained largely ice-free. Species residing in this region were thus less likely to be fragmented during the ice ages. The situation is drastically different in the western Palearctic and the Nearctic. Here, huge ice sheets extended to lower latitudes, pushing bird populations into several refugia in the south. The climatic differences between these regions need to be taken into account when reconstructing the evolutionary history of the local bird species.

All in all, this study highlights the importance of considering both the effects of glacial and interglacial periods in the evolution of shorebirds. And it emphasizes the significant climatic differences between biogeographical regions.

An overview of the different biogeographical regions. The Palearctic (red) and Nearctic (green) are most relevant here. © Carol | Wikimedia Commons.


Arcones, A., Ponti, R., Ferrer, X., & Vieites, D. R. (2021). Pleistocene glacial cycles as drivers of allopatric differentiation in Arctic shorebirds. Journal of Biogeography48(4), 747-759.

Featured image: Red Knot (Calidris canutus) © Hans Hillewaert | Wikimedia Commons

Are the Blue-faced and the Papuan Parrotfinch different species or not?

These birds are morphologically distinct, but have similar mitochondrial DNA.

Last year, I covered a study on the phylogeny of the estrildid finches (family Estrildidae). The original paper included samples of the Blue-faced Parrotfinch (Erythrura trichroa) and the Papuan Parrotfinch (Erythrura papuana). The authors – Urban Olsson and Per Alström – noticed that these two samples shared the same mitochondrial haplotype. They briefly commented that this result could be due to misidentified specimens and did not pay further attention to these samples. There might, however, be an interesting biological explanation for the identical haplotypes of these samples. Hence, a recent study in the Bulletin of the British Ornithologists’ Club took a closer look at these Parrotfinches.

Bill Morphology

Initially, the Papuan Parrotfinch was described as a subspecies of the Blue-faced Parrotfinch by Rotschild and Hartert. Later on, Hartert elevated the Papuan Parrotfinch to species level, based on differences in bill morphology. He drew parallels with the Darwin’s Finches by writing that “We have thus a similar case as in the genus Geospiza on the Galapagos Islands, a large and a small form occurring together.” Indeed, the bill of the Papuan Parrotfinch is significantly larger than that of its Blue-faced relative. However, a difference in morphology does not necessarily mean that we are dealing with distinct species. For example, in the African genus Pyrenestes, you can observe three distinct phenotypes in a genetically uniform population. The differences in morphology are due to adaptation to different resources. Could the same process be at work in the Parrotfinches?

The difference in bill morphology between the Papuan Parrotfinch (left) and the Blue-faced Parrotfinch (right). From: DeCicco et al. (2020) Bulletin of the British Ornithologists’ Club.

Three Scenarios

To solve this mystery, Lucas DeCicco and his colleagues sequenced the mitochondrial gene ND2 and compared the morphology of several specimens. They found that the Papuan Parrotfinch and the Blue-faced Parrotfinch were almost identical in the sequence of ND2, whereas they showed no overlap in several morphological measurements. This finding can be explained in several ways, nicely summarized in the discussion section:

(1) morphological differences arose in allopatry with either limited genetic divergence or gene flow upon secondary sympatry, (2) sympatric or ecological speciation is occurring with strong selection on different phenotypes, or (3) these two phenotypes represent a single panmictic population with a phenotypic polymorphism.

At the moment, we cannot draw a definitive conclusion yet. More genetic data – nuclear genes or genomic data – is needed to discriminate between these three scenarios. This study does provide the first step in unraveling the evolutionary history of these birds, showing that the result of Urban Olsson and Per Alström was not due to a misidentification. Instead, the sharing of mitochondrial haplotypes has a biological explanation. Which one remains to be determined. This how science works, slowly collecting pieces of the puzzle until we can see the bigger picture.

The two species clearly differed in several morphological measurements. From: DeCicco et al. (2020) Bulletin of the British Ornithologists’ Club.


DeCicco, L. H., Benz, B. W., DeRaad, D. A., Hime, P. M., & Moyle, R. G. (2020). New Guinea Erythrura parrotfinches: one species or two?. Bulletin of the British Ornithologists’ Club140(3), 351-358.

Featured image: Blue-faced Parrotfinch (Erythrura trichroa) © Nrg800 | Wikimedia Commons

Are Black Kite hybrids moving into Europe?

Photographs reveal more birds with features from an eastern subspecies.

Did you know there are three subspecies of Black Kite (Milvus migrans) across Eurasia? The western subspecies (migrans) can be found from Europe into Russia, where it is replaced by the eastern subspecies (lineatus, also known as the Black-eared Kite). The third subspecies (govinda) occurs in India and Southeast Asia. All three subspecies overlap in distribution and might interbreed in these contact zones. In his book on European raptors, Dick Forsman stated that Black Kites with characteristics of the eastern subspecies (lineatus) were increasing in Europe. These birds might represent hybrids from the contact zone between the western and eastern subspecies. A recent study in the Journal of Ornithology tested the claim by Dick Forsman by analyzing the pictures of Black Kites in Europe. The researchers used a set of morphological features to discriminate between the different subspecies and potential hybrids.

Distribution of different Black Kite subspecies. From: Andreyenkova et al. (2019).


The careful analyses of numerous pictures revealed observations of 65 Black Kites with lineatus-features in Europe. The sightings of these peculiar birds increased over time, with a notable rise in 2018 and 2019. An interesting result that raises many questions. First, does this pattern really represent more lineatus-like birds moving into Europe? Or can this result be explained by a significant increase in the number of birdwatchers and photographers (with better equipment) in Europe? More systematic monitoring of Black Kites – perhaps even using GPS-trackers – might be needed to better understand the movements of these birds.

Second, are these lineatus-like birds really hybrids? The researchers mention that carotenoid supplementation in the food can enhance the yellow color in the beak and legs of the birds (an important feature in identifying these hybrids). Intermediate coloration of these traits can thus be explained by both hybridization and diet. Again, more research is warranted here. In addition, there is a lot of overlap in morphological characters between these subspecies. It is thus possible that there is clinal variation across the range of the Black Kites. Taxonomists have classified the extremes of this cline as distinct subspecies (migrans and lineatus), but there might be a whole range of intermediate phenotypes. Indeed, a recent opinion piece in the journal Ibis highlighted the difficulties of clinal variation in taxonomic decisions. We need more insights into the morphological and genetic variation across the entire range of the Black Kite before we can confidently assess whether the lineatus-like birds in Europe represent hybrids or not. An exciting question to explore.

An increasing number of Black Kites with lineatus features have been observed in Europe. From: Skyrpan et al. (2021) Journal of Ornithology.


Skyrpan, M., Panter, C., Nachtigall, W., Riols, R., Systad, G., Škrábal, J., & Literák, I. (2021). Kites Milvus migrans lineatus (Milvus migrans migrans/lineatus) are spreading west across Europe. Journal of Ornithology162(2), 317-323.

Featured image: Black Kite (Milvus migrans) © Вых Пыхманн | Wikimedia Commons

Divergent sperm morphology as a reproductive barrier between Saltmarsh and Nelson’s Sparrow

But is the difference large enough to interfere with fertilization?

Along the east coast of North America, two small songbirds are interbreeding: the Saltmarsh Sparrow (Ammospiza caudacuta) and the Nelson’s Sparrow (A. nelsoni). Despite high levels of interspecific gene flow, these species remain largely distinct. What reproductive isolation mechanisms could prevent these sparrows from merging into one species? One possible explanation concerns adaptation to different ecological conditions: the Saltmarsh Sparrow is restricted to coastal marshes, whereas the Nelson’s Sparrow can be found in a larger variety of habitats. Hybrids might not be able to survive in certain environments. Another putative reproductive barrier could be related to differences in mating behavior. Male Nelson’s Sparrows attract females by singing and performing song flights. After a successful copulation, they tend to guard the female for a short time. Male Saltmarsh Sparrows, on the other hand, do not perform such courtship displays, but rather chase females around. Hybrids might show intermediate behaviors and will not be able to secure a mate. A recent study in the journal Ecology and Evolution examined a third reproductive barrier: sperm morphology.

Sperm Size

Female birds store sperm in specialized organs (so-called tubules). If the morphology of the sperm does not match the shape of these organs, the sperm will not be stored and can thus not be used for fertilization. If the differences in sperm morphology are small enough, this issue can be overcome and might lead to the production of hybrids. However, the resulting hybrids might experience fertility issues. The sperm cells of hybrids might be abnormally shaped and not functional, leading to sterile males (as in Flycatchers). Or hybrids can have perfectly viable sperm cells that are unable to fertilize the egg due to genetic mismatches (which is possibly the case in Long-tailed Finches). To check the situation in the Ammospiza Sparrows, Emily Cramer and her colleagues studied the sperm morphology of nine Saltmarsh Sparrows, nine Nelson’s Sparrows and four intermediate birds.

The data collection revealed that the sperm of the putative hybrids was fine. They did not show any abnormal sperm cells and are thus most likely fertile. In fact, the intermediate birds produced more sperm than both parental species (I will come back to this intriguing observation later on). But what about the sperm morphology? The analyses showed that the sperm cells of Saltmarsh Sparrows were about 4 percent longer than those of Nelson’s Sparrows. Whether this difference is sufficiently large to interfere with fertilization remains to be investigated. Indeed, the researchers indicate that a study of the female reproductive tract will be a logical next step.

There was a clear difference in the size of sperm cells between both species (top figure). Interestingly, the size of the sperm cells correlated nicely with the plumage scores of the birds (bottom figure). From: Cramer et al. (2021) Ecology and Evolution.

Plumage Scores

The researchers also noted a strong correlation between the plumage score of the birds and the size of the sperm cells. They speculate that this result could reflect some fitness consequences for the male birds. Plumage might reflect the sperm phenotype, allowing female birds to better judge males and obtain compatible sperm. This connection between a male’s phenotype and his fertility has been suggested by Ben Sheldon. He focused on variation within species, but this mechanism might extend across species boundaries. If females do indeed focus on plumage patterns to select males, the hybrids might be at a disadvantage due to their intermediate plumages. Hybrids will then copulate less, which might explain the higher sperm count in this study. The intermediate birds had not copulated recently, resulting in fuller sperm stores. The authors summarize the situation nicely in the discussion: “intermediate males suffer from reduced copulation success, but not reduced fertilization success”.


Cramer, E. R., Grønstøl, G., Maxwell, L., Kovach, A. I., & Lifjeld, J. T. (2021). Sperm length divergence as a potential prezygotic barrier in a passerine hybrid zone. Ecology and Evolution, 11: 9489-9497.

Featured image: Nelson’s Sparrow (Ammospiza nelsoni) © Andy Reago & Chrissy McClarren | Wikimedia Commons

Unraveling the evolutionary history of the Galapagos Rail

When did this species reach the Galapagos Islands and where did it come from?

As more and more bird genomes are being sequenced (see this paper for the latest overview), it is surprising to come across bird species without genetic resources. But these species do exist, such as the Galapagos Rail (Laterallus spilonota). The lack of genetic studies on this rail might be an even bigger surprise when you took a closer look at its common name: this species occurs on the Galapagos, one of the most studied island archipelagos in the world. While some charismatic or historically relevant species attracted a lot of scientific attention – just think of the iconic Darwin’s Finches – the Galapagos Rail has not been studied with genetic tools yet. Hence, we know little about the evolutionary history of this rail and, more importantly, we have almost no knowledge about its conservation status from a genetic point of view. The Galapagos Rail might be heading for extinction and we would not have a clue. Luckily, a recent study in the journal Diversity provided the first genetic assessment of the Galapagos Rail.


Jaime Chaves and his colleagues sequenced the DNA of several recent and historical samples to reconstruct the evolutionary history of the Galapagos Rail. Phylogenetic analyses revealed that the ancestor of this species reached the Galapagos Islands about 1.2 million years ago. This timing is similar to other species, for example Darwin’s Finches arrived between 1 and 1.5 million years ago. The sister species of the Galapagos Rail turned out to be the Black Rail (Laterallus jamaicensis), which currently has a patchy distribution across North America and along the coast of Peru and Chile. The exact source population of Black Rails that gave rise to the Galapagos Rail remains to be determined with further sampling. It seems likely that the Galapagos Rail arose from birds dispersing out of the South American populations, but it is also possible that individuals migrating from North to Central America were blown off course and ended up on the Galapagos. Or perhaps an extinct “ghost” population was involved (such as in the Red-billed Chough). Plenty of hypotheses to explore.

The Galapagos Rail (#1) is most closely related to the Black Rail (#4) from which it split about 1.2 million years ago. From: Chaves et al. (2020) Diversity.

Genetic Diversity

More detailed analyses indicated little genetic differentiation between the island populations of the Galapagos Rail. This finding is rather surprising because this species is flightless and is thus not expected to disperse very far. The authors noted that these rails have been observed to forage near the coast and that they are capable of swimming significant distances. So, frequent movements between islands – which are on average 25 kilometers apart – are not impossible.

The researchers also reported low levels of genetic diversity in the Galapagos Rail, which can be explained by recent population bottlenecks. This species has suffered from human activities, such as habitat loss due to agricultural expansion and the introduction of non-native predators (mostly cats and rats). Currently, the Galapagos Rail can be found in higher numbers within restored habitats. They might thus recover from past population bottlenecks, although they still carry the genetic signatures of these events. Nonetheless, the information from this genetic study can help guide future conservation efforts to preserve the Galapagos Rail.

Only a few haplotypes (shared across different islands) were found for the different genetic markers. This low level of genetic diversity is probably due to past population bottlenecks. From: Chaves et al. (2020) Diversity.


Chaves, J. A., Martinez-Torres, P. J., Depino, E. A., Espinoza-Ulloa, S., García-Loor, J., Beichman, A. C., & Stervander, M. (2020). Evolutionary history of the Galápagos Rail revealed by ancient mitogenomes and modern samples. Diversity12(11), 425.

Featured image: Galapagos Rail (Laterallus spilonota) © John Gould | Wikimedia Commons