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The origin of the seedeaters

Studies capture the process through which 11 species of a South American bird group emerged




Genetic material and the physical appearance of 11 species of seedeaters—small birds from open areas of South America that eat seeds and, along with their finch cousin, belong to the genus Sporophila—tell a unique evolutionary story that is still unfolding and, therefore, difficult to pin down. Recent studies that sequenced several segments of their genomes indicate that eight of these species—only those that likely emerged more recently and live in close proximity to one another, sometimes sharing the same habitat—have retained highly similar DNA that is indistinguishable for taxonomic identification purposes. Genome segments from one species are mixed in with segments from another, forming a molecular mosaic.

Nevertheless, the males of the two species exhibit distinct differences in morphology, particularly in their color patterns and vocalizations. “The plumage and song of birds evolve faster than most genetic differences,” says Luís Fábio Silveira, curator of the ornithology department at the University of São Paulo Zoology Museum (MZ-USP), who has authored recent papers on seedeaters. His co-author is Argentine evolutionary biologist Leonardo Campagna, who is pursuing postdoctoral studies in the Ornithology Laboratory at Cornell University. Only the three oldest species—the Chestnut-bellied Seedeater (S. castaneiventris), the Ruddy-breasted Seedeater (S. minuta) and the Capped Seedeater (S. bouvreuil)—have accumulated differences in their DNA significant enough that molecular analysis can differentiate them from one another and from other species.

The Chestnut-bellied Seedeater and the Ruddy-breasted Seedeater live in different areas of northern South America, and their populations almost never have contact with specimens of the eight younger species. The Capped Seedeater, the most abundant of these species, is found in the Brazilian state of Pará, throughout the country’s Northeast and Southeast regions, and in parts of the Central-West (see map showing the geographic distribution of the various species). Its area of occurrence intersects at some points with that of the other species. “The part of the genome that produces the morphological differences between the species is probably small,” says Campagna. In June 2014, a study published in the journal Nature showed that the DNA of two European crow species, the Carrion Crow (Corvus corone) and the Hooded Crow (Corvus cornix), were practically identical. The difference amounted to less than 0.28% of the genome, despite the color distinctions characteristic of each bird.

A male Pearly-bellied Seedeater courts a female: the bird recognizes a partner from its own species

A male Pearly-bellied Seedeater courts a female: the bird recognizes a partner from its own species

According to the papers by Silveira and Campagna, S. bouvreuil is the closest living relative of the eight younger species of seedeater, which dwell in southern Brazil, Uruguay, Paraguay, northern Argentina and eastern Bolivia. “It was previously thought that S. minuta was the closest relative,” says Campagna. These more recently-evolved species, thought to have emerged between 1.2 million and 500,000 years ago, are the Tawny-bellied Seedeater (S. hypoxantha), the Black-bellied Seedeater (S. melanogaster), the Dark-throated Seedeater (S. ruficollis), the Marsh Seedeater (S. palustris), the Black-and-tawny Seedeater (S. nigrorufa), the Chestnut Seedeater (S. cinnamomea), the Grey-and-chestnut Seedeater (S. hypochroma) and the Pearly-bellied Seedeater (S. pileata). The first five of these birds are endangered species. The two researchers, who studied seedeaters separately until they decided to work collaboratively in 2013, have published two studies on this group of birds. The first paper appeared in the journal The Auk in 2013, and the second was published in Molecular Ecology in August 2015. All types of seedeaters are approximately 10 centimeters in length, weigh 7 grams, and are appreciated for their beautiful song.

044-049_Aves_236-02Similar-looking females
Unlike the males, the females and young of these 11 seedeater species are quite similar in outward appearance, with plumage of less striking colors. This makes it difficult to identify the species of a female or young specimen solely on the basis of that parameter. Generally speaking, the females have a darker, brownish back and a lighter belly, in shades of olive. Since hybrids among these 11 species are practically nonexistent in nature, researchers believe the birds have some mechanism—perhaps song and geographic distribution—that enables them to recognize a sexual partner of their own species so they can reproduce with the proper partners. There is also some evidence that the females’ plumage may display shades in the ultraviolet wavelength, invisible to the human eye but not to birds. This may be an additional mechanism for recognition among species.

Silveira is raising all 11 species in cages at his home in São Paulo, with the objective of understanding the mechanisms that govern reproduction in the different types of seedeater. When a pair of birds mates and produces healthy offspring, the ornithologist assumes that the female has found a male of her species. He then separates the pair for further study. If the newborn birds die after a while, it probably resulted from cross-breeding between two different species that have lost the ability to produce healthy hybrids. “You can’t discount the existence of seedeater hybrids, even though it’s hard to identify the species of juvenile specimens, but I’ve never found one of them in nature,” Silveira points out. Another feature that hampers species recognition is the fact that the males periodically lose their characteristically colorful plumage before they migrate to northern Brazil to escape the cold southern winter, and at these times they look similar to the females.

Species of Galapagos finch, with a broad beak...

Species of Galapagos finch, with a broad beak…

The two researchers believe this is a complex case of ongoing speciation, an evolutionary process in which a population of a hypothetical ancestral species diverges into other species. “This is a story that has been evolving for a few million years,” Campagna says. For now, genetic studies and analyses of the morphology and geographic distribution of the species make it possible to outline an approximate scenario of the likely evolutionary history of the South American seedeaters. The genus Sporophila, which literally means seedeater, currently comprises 38 species. After the emergence of the Isthmus of Panama—the geological event that connected the two halves of the continent a few million years ago (estimates vary from 3 million to 12 million years), specimens of Sporophila radiated throughout Central and North America. Silveira and Campagna worked on a subset of the overall genus, the 11 species known as southern capuchinos.

Most of these species were described in the 18th and 19th centuries, so they were elevated to species status more than a century ago, when taxonomists differentiated birds primarily by their outward appearance, song, habitat and behavior. “Their skeletons are identical, and furthermore it is impossible to distinguish the species through bone analysis,” Silveira comments. In many cases, the bird’s popular name highlights its principal physical feature—the distinctive characteristic that enables taxonomists to recognize them from among similar species. The Dark-throated Seedeater, for example, has a black patch below the beak, and the Pearly-bellied Seedeater has the most white plumage.

According to the two researchers’ recent papers, which analyzed the mitochondrial DNA (inherited only from the mother) and 3,000 molecular markers present in the DNA of this bird group, the oldest known representative of this lineage is the Chestnut-bellied Seedeater, which occurs in northern South America. The seedeaters diversified and fashioned an evolutionary journey that would also lead them to occupy the southern part of the subcontinent. Down through the evolutionary process, another ancestral population may have adapted and produced the Ruddy-breasted Seedeater, whose quintessential habitat is the Amazon Region. The stock that produced this species may also have given rise to the Capped Seedeater, which inhabits a vast stretch of the Brazilian Northeast and Southeast and was likely responsible for producing a wide range of forms as it gradually occupied new, southern areas of the subcontinent. “At least eight species emerged more or less at the same time. They shared a common ancestor with S. bouvreuil and, prior to that, they shared another common ancestor among themselves,” says Campagna.

...and with a thin beak: Darwin noted the difference in the 19th century, and a recent study has identified the gene associated with that physical trait

…and with a thin beak: Darwin noted the difference in the 19th century, and a recent study has identified the gene associated with that physical trait

In some cases, modern genetic studies of populations enable scientists to calculate when a species is likely to have emerged. Silveira and Campagna estimate that the species derived from the Capped Seedeater took form between 1.2 million and 500,000 years ago. Estimates suggest that at that time, the populations of the genus Sporophila increased tenfold. The enormous size of this ancestral group has been cited as one possible explanation for the fact that it is still impossible to see any clear distinctions in the DNA of the more recent forms of seedeaters. “Species derived from very large populations take longer to fix their differences into the genome,” the Argentine biologist notes. This phenomenon is owed to the effects of genetic drift, which in each generation causes some individuals to inherit certain characteristics purely at random (rather than by natural selection, some form of mutation or population migration). The effects of genetic drift are slower in groups derived from large populations.

The story of the seedeaters recalls that of another group of birds, the finches of the Galapagos Islands in Ecuador. These birds have become a classic example of the process of speciation and evolutionary adaptation, having been cited in the book The Origin of Species by Charles Darwin (1809-1882), who laid the groundwork for the theory of natural selection. The English naturalist noted that the shape of the beak in finches varied among the different islands of the Pacific archipelago. Subsequent evolutionary studies have shown that this physical trait varies according to the type of food available in the finches’ habitat, competition among species and geographic isolation. On many of the islands in the Pacific archipelago, there are finches with beaks of different shapes, adapted to the local food supply. Continental finches, for example, tend to have broader beaks that enhance their ability to break open seeds. Darwin’s finches have thin, pointed beaks, better adapted for spearing insects.

Carrion Crow...

Carrion Crow…

British evolutionary biologists Peter and Rosemary Grant, professors emeritus at Princeton University, said in their most recent book, 40 years of evolution: Darwin’s finches on Daphne Major Island, published in 2014, that seedeaters appear to be a sort of terra firma version of Darwin’s finches. “In several respects capuchinos may be the continental equivalent of Darwin’s finches,” wrote the Grants, who for four decades have spent six months of every year in the Galapagos. The pair were also co-authors of a paper from Uppsala University, Sweden, published in Nature in February 2015, which revealed the whole-genome sequencing of the 14 species of Galápagos finches and one species from Cocos Island, a Pacific dependency of Costa Rica. Their findings included the identification of the ALX1 gene as one of those responsible for the shape of the birds’ beaks.

Species or morphological variation
Not all taxonomists concur with the idea that the 11 different types of seedeater should be regarded as distinct species. Although the morphology, some habits and geographic distribution present specific traits, at least eight species are practically identical from a molecular standpoint. “If there are no genetic alterations that explain the differences in phenotype, there is no reason to consider some forms of seedeater as a species,” says biologist Miguel Trefaut Rodrigues, a taxonomist and reptile specialist at the USP Biosciences Institute, who is a friend of Silveira. “Classifying living creatures is always difficult. But genetics makes the work less inexact.” In his view, the eight newest species of seedeater, whose DNA is indistinguishable within the group, should be considered a single species that exhibits different morphologies, in this case a distinct color pattern in the plumage.

...and Hooded Crow: the two European crow species have different plumage color, but their genomes differ by less than 0.28%

…and Hooded Crow: the two European crow species have different plumage color, but their genomes differ by less than 0.28%

Evolutionary biologist Fábio Raposo do Amaral, a professor at the Federal University of São Paulo (Unifesp), Diadema campus, prefers not to delve into the merits of the question of whether the most recent forms of seedeater should be considered different species or a morphological variation (i.e., difference in outward appearance) of a single species. “In the recent past, we were naive and thought that genomics would automatically settle the most complex taxonomic questions,” says Amaral, who works with birds. “But seedeaters are an intermediate case, in which there is a mismatch between morphological variation and genetics. Even with large datasets in hand, we still have a lot to learn about how species emerge.”

Silveira and Campagna hope to conduct new studies that might enable them to find molecular signatures in the genome of each species in the genus, perhaps the genes responsible for some specific trait, as they did with the gene linked to beak formation in Darwin’s finches. “Our idea is to sequence segments of the genome that may be linked to color production in the feathers of each species,” Silveira says.

Scientific articles
CAMPAGNA, L. et al. Identifying the sister species to the rapid capuchino seedeater radiation (Passeriformes: Sporophila). Auk. V. 130, No. 4, p.645-55. October 2013.
CAMPAGNA, L. et al. Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation. Molecular Ecology. V. 24, No. 16, p. 4238-51. August 2015.

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