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Sporophila (1 Viewer)

Campagna, Repenning, Silveira, Fontana, Tubaro, Lovette. [2016.] Repeated divergent selection on pigmentation genes in a rapid finch radiation driven by sexual selection.
[preprint on BioRχiv]

Campagna, Repenning, Silveira, Fontana, Tubaro, Lovette. Repeated divergent selection on pigmentation genes in a rapid finch radiation. Science Advances 24 May 2017: Vol. 3, no. 5, e1602404
DOI: 10.1126/sciadv.1602404
 
Sporophila torqueola

Mason NA, Olvera-Vital A, Lovette IJ, Navarro-Sigüenza AG. Hidden endemism, deep polyphyly, and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White-collared Seedeater complex (Thraupidae: Sporophila torqueola). Ecol Evol. 2018;00:1–15. https://doi.org/10.1002/ece3.3799

Abstract:

Phenotypic and genetic variation are present in all species, but lineages differ in how variation is partitioned among populations. Examining phenotypic clustering and genetic structure within a phylogeographic framework can clarify which biological processes have contributed to extant biodiversity in a given lineage. Here, we investigate genetic and phenotypic variation among populations and subspecies within a Neotropical songbird complex, the White-collared Seedeater (Sporophila torqueola) of Central America and Mexico. We combine measurements of morphology and plumage patterning with thousands of nuclear loci derived from ultraconserved elements (UCEs) and mitochondrial DNA to evaluate population differentiation. We find deep levels of molecular divergence between two S. torqueola lineages that are phenotypically diagnosable: One corresponds to S. t. torqueola along the Pacific coast of Mexico, and the other includes S. t. morelleti and S. t. sharpei from the Gulf Coast of Mexico and Central America. Surprisingly, these two lineages are strongly differentiated in both nuclear and mitochondrial markers, and each is more closely related to other Sporophila species than to one another. We infer low levels of gene flow between these two groups based on demographic models, suggesting multiple independent evolutionary lineages within S. torqueola have been obscured by coarse-scale similarity in plumage patterning. These findings improve our understanding of the biogeographic history of this lineage, which includes multiple dispersal events out of South America and across the Isthmus of Tehuantepec into Mesoamerica. Finally, the phenotypic and genetic distinctiveness of the range-restricted S. t. torqueola highlights the Pacific Coast of Mexico as an important region of endemism and conservation priority.

[pdf]
 
Sporophila maximiliani

Taxonomy, natural history, and conservation of the Great-billed Seed-Finch Sporophila maximiliani (Cabanis, 1851) (Thraupidae, Sporophilinae)
FLÁVIO KULAIF UBAID, LUÍS FABIO SILVEIRA, CESAR A. B. MEDOLAGO, THIAGO V. V. COSTA, MERCIVAL ROBERTO FRANCISCO, KARLLA V. C. BARBOSA, ADIR D. S. JÚNIOR

Abstract

Seed-finches are small-sized Neotropical granivorous birds characterized by extremely strong and thick beaks. Among these birds, the Great-billed Seed-Finch Sporophila maximiliani has been selectively and intensively trapped to the extent that has become one of the most endangered bird species in South America, yet its taxonomy remains complex and controversial. Two subspecies have been recognized: S. m. maximiliani (Cabanis, 1851), mainly from the Cerrado of central South America, and S. m. parkesi Olson (= Oryzoborus m. magnirostris), from northeastern South America. Originally, S. m. parkesi was diagnosed as being larger than the Large-billed Seed-Finch, S. c. crassirostris (Gmelin, 1789), but proper comparisons with S. m. maximiliani, which is larger than S. c. crassirostris, were never performed. Here we provide a review of the taxonomic and nomenclatural history of S. maximiliani, reevaluate the validity and taxonomic status of the subspecies based on morphological characters, and significantly revise its geographic distribution. Analyses based on plumage patterns and a Principal Component Analysis of morphometric characters indicated that S. m. parkesi is most appropriately treated as a synonym of the nominate taxon, which results in a monotypic S. maximiliani comprising two disjunct populations. Further, we conducted systematic searches for S. maximiliani in Brazil, in an attempt to obtain natural history information. After more than 6,000 hours of fieldwork in 45 areas of potential and historical occurrence, S. maximiliani was located only in two sites, in marshy environments called veredas, confirming the critical conservation status of this species, at least in Brazil. We discuss the conservation potential for, and the problems involved with, captive breeding of S. maximiliani for reintroduction into the wild.

http://www.mapress.com/j/zt/article/view/zootaxa.4442.4.4
 
Sporophila torqueola

TiF Update August 2:

The White-collared Seedeater, Sporophila torqueola has been split into Morellet's Seedeater / White-collared Seedeater, Sporophila morelleti and and Cinnamon-rumped Seedeater, Sporophila torqueola based on the AOS 59th Supplement and Mason et al. (2018). As with the Juncos above, they are not sister taxa.
 
He is back!
Note from 59th AOS Supplement.
Notes.—The scientific name honors the collector of the
type specimen, P. M. A. Morelet (Salvin and Godman
1885), but Bonaparte misspelled his name in the species
description, an error perpetuated in the English name
‘‘Morellet’s Seedeater’’ by AOU (1886), Ridgway (1901), and
others.
Pendantcy is a sickness.
 
Last edited:
Hussein A. Hejase, Ayelet Salman-Minkov, Leonardo Campagna, Melissa J. Hubisz, Irby J. Lovette, Ilan Gronau, and Adam Siepel. Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. PNAS first published November 16, 2020; https://doi.org/10.1073/pnas.2015987117

Abstract:

Numerous studies of emerging species have identified genomic “islands” of elevated differentiation against a background of relative homogeneity. The causes of these islands remain unclear, however, with some signs pointing toward “speciation genes” that locally restrict gene flow and others suggesting selective sweeps that have occurred within nascent species after speciation. Here, we examine this question through the lens of genome sequence data for five species of southern capuchino seedeaters, finch-like birds from South America that have undergone a species radiation during the last ∼50,000 generations. By applying newly developed statistical methods for ancestral recombination graph inference and machine-learning methods for the prediction of selective sweeps, we show that previously identified islands of differentiation in these birds appear to be generally associated with relatively recent, species-specific selective sweeps, most of which are predicted to be soft sweeps acting on standing genetic variation. Many of these sweeps coincide with genes associated with melanin-based variation in plumage, suggesting a prominent role for sexual selection. At the same time, a few loci also exhibit indications of possible selection against gene flow. These observations shed light on the complex manner in which natural selection shapes genome sequences during speciation.
 
Cecilia Estalles, Sheela P. Turbek, María José Rodríguez-Cajarville, Luís Fábio Silveira, Kazumasa Wakamatsu, Shosuke Ito, Irby J. Lovette, Pablo L. Tubaro, Darío A. Lijtmaer, and Leonardo Campagna. 2022. Concerted variation in melanogenesis genes underlies emergent patterning of plumage in capuchino seedeaters. Proceedings of the Royal Society B, published 12 January 2022.
https://doi.org/10.1098/rspb.2021.2277

Abstract
Coloration traits are central to animal communication; they often govern mate choice, promote reproductive isolation and catalyse speciation. Specific genetic changes can cause variation in coloration, yet far less is known about how overall coloration patterns—which involve combinations of multiple colour patches across the body—can arise and are genomically controlled. We performed genome-wide association analyses to link genomic changes to variation in melanin (eumelanin and pheomelanin) concentration in feathers from different body parts in the capuchino seedeaters, an avian radiation with diverse colour patterns despite remarkably low genetic differentiation across species. Cross-species colour variation in each plumage patch is associated with unique combinations of variants at a few genomic regions, which include mostly non-coding (presumably regulatory) areas close to known pigmentation genes. Genotype–phenotype associations can vary depending on patch colour and are stronger for eumelanin pigmentation, suggesting eumelanin production is tightly regulated. Although some genes are involved in colour variation in multiple patches, in some cases, the SNPs associated with colour changes in different patches segregate spatially. These results suggest that coloration patterning in capuchinos is generated by the modular combination of variants that regulate multiple melanogenesis genes, a mechanism that may have promoted this rapid radiation.
 
Rapid diversification of the Variable Seedeater superspecies complex despite widespread gene flow
Diego Ocampo, Kevin Winker, Matthew J Miller, Luis Sandoval, J Albert C Uy
DOI: 10.1016/j.ympev.2022.107510


Abstract
Disentangling the evolutionary relationships of rapidly radiating clades is often challenging because of low genetic differentiation and potentially high levels of gene flow among diverging taxa. The genus Sporophila consists of small Neotropical birds that show, in general, relatively low genetic divergence, but particularly high speciation rates and pronounced variation in secondary sexual traits (e.g., plumage color), which can be important in generating premating reproductive isolation. In cases like these, the use of genome-wide sequence data can increase the resolution to uncover a clade's evolutionary history. Here, we used a phylogenomic approach to study the evolutionary history and genetic structure of the Variable Seedeater superspecies complex, which includes S. corvina, S. intermedia, and S. americana. Using ∼25,000 genome-wide single nucleotide polymorphisms (SNPs), we confirmed that the Variable Seedeater superspecies complex is monophyletic. However, a phylogenetic reconstruction based on a mitochondrial marker (ND2) resulted in a discordant tree topology, particularly in the position of Wing-barred Seedeater S. americana, which might be due to a mitochondrial capture event. Our results suggest historical gene flow among lineages, particularly between species with conflicting topologies. Among the four phenotypically variable S. corvina subspecies, our structure analyses identified three main distinct genetic groups (K = 3), and that the entirely black subspecies, S. c. corvina, is derived from within a pied-colored clade. Further, we inferred widespread gene flow across the whole species' distribution, including between subspecies. However, gene flow was about 100 times lower at the geographic boundaries of the entirely black and the pied subspecies, suggesting an important role for plumage divergence in limiting gene flow. Overall, our findings suggest that the early diversification of the Sporophila genus occurred rapidly despite historical gene flow between lineages and that divergence in plumage color possibly influences the extent of gene flow among taxa.
 
Nguyen, T.N., M. Repenning, C.S. Fontana, and L. Campagna (2024)
Genomic islands of speciation harbor genes underlying coloration differences in a pair of Neotropical seedeaters
Evolution (advance online publication)
doi: 10.1093/evolut/qpae051

Incomplete speciation can be leveraged to associate phenotypes with genotypes, thus providing insights into the traits relevant to the reproductive isolation of diverging taxa. We investigate the genetic underpinnings of the phenotypic differences between Sporophila plumbea and S. beltoni. S. beltoni has only recently been described based, most notably, on differences in bill coloration (yellow vs. black in S. plumbea). Both species are indistinguishable through mtDNA or reduced-representation genomic data, and even whole-genome sequencing revealed low genetic differentiation. Demographic reconstructions attribute this genetic homogeneity to gene flow, despite divergence in the order of millions of generations. We found a narrow hybrid zone in southern Brazil where genetically, yet not phenotypically, admixed individuals appear to be prevalent. Despite the overall low genetic differentiation, we identified three narrow peaks along the genome with highly differentiated SNPs. These regions harbor six genes, one of which is involved in pigmentation (EDN3) and is a candidate for controlling bill color. Within the outlier peaks we found signatures of resistance to gene flow, as expected for islands of speciation. Our study shows how genes related to coloration traits are likely involved in generating prezygotic isolation and establishing species boundaries early in speciation.
 

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