Extreme mitogenomic divergence between two syntopic specimens of
            <i>Arremon aurantiirostris</i>
            (Aves: Emberizidae) in central Panama suggests possible cryptic species

López, Krisangel; Angeli, Cody; Aguilar, Celestino; Loaiza, José R.; León, Luis F. De; McMillan, W. Owen; Miller, Matthew J.

doi:10.3109/19401736.2015.1066344

Cited by 2 publications

(3 citation statements)

References 14 publications

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“…Mitochondrial barcoding provides us with a powerful tool to detect cryptic diversity (Arnot, Roper, and Bayoumi 1993;Floyd et al 2002;Hebert, Ratnasingham, and deWaard 2003;Hebert and Gregory 2005;Clare et al 2007;Vasconcelos et al 2016;Imtiaz, Nor, and Naim 2017;Bernstein et al 2021). Previous efforts using mitochondrial markers have documented cryptic variation in multiple Panamanian birds (González et al 2003;Miller et al 2008;Bryson et al 2014;Loaiza et al 2016;Lopez et al 2016). However, as useful as single-taxon studies are, they provide only one example of potential widespread patterns of phylogeographic diversity.…”

Section: Introductionmentioning

confidence: 99%

“…Both the communities of these discrete regions and the more continuously distributed lowland taxa may have been subject to historic isolation, especially prior to the final closure of the Isthmus of Panama approximately 2.7 to 4.2 million years ago (Leigh, O'Dea, and Vermeij 2014b;O'Dea et al 2016;Jaramillo et al 2017), or by the possible expansion of savannah habitats and formation of forest refugia during the Pleistocene (Smith, Amei, and Klicka 2012). In particular, lowland Panama has been recognized as a hotspot for species turnover-replacement of a given taxa with other taxa-in birds (Miller, Bermingham, and Ricklefs 2007;Loaiza et al 2016;Lopez et al 2016;McLaughlin, Garzón, et al 2020), as well as in freshwater fish (Bermingham and Martin 1998;Martin and Bermingham 2000;Perdices et al 2002;Smith and Bermingham 2005;Bagley and Johnson 2014), mammals (Cortés-Ortiz et al 2003), herpetofauna (Crawford 2003;Crawford and Smith 2005;Bagley and Johnson 2014), insects (Bagley and Johnson 2014;Eskildsen et al 2018), and plants (Dick, Abdul-Salim, and Bermingham 2003). Thus, using barcoding, we can investigate if biogeography is an important factor in generating avian diversity, by testing if divergence events are broadly coincident in time (Naka and Brumfield 2018).…”

Section: Introductionmentioning

confidence: 99%

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Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds

McLaughlin

Aguilar

Bernstein

et al. 2023

Preprint

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Defining phenotypically similar populations as separate cryptic species can provide insights into the speciation process, as the taxa in question are often in the early stages of speciation. Here, we identify potential cryptic species based on a comprehensive dataset of COI mitochondrial DNA barcodes from 2,333 individual Panamanian birds across 429 species, representing 391 (59%) of the 659 resident landbird species of the country, as well as opportunistically sampled waterbirds. We complement this dataset with additional publicly available mitochondrial loci, such as ND2 and cytochrome b, obtained from whole mitochondrial genomes from 20 taxa. Using barcode identification numbers (BINs), we find putative cryptic species in 19% of landbird species, highlighting hidden diversity in the relatively well-described avifauna of Panama. Whereas some of these mitochondrial divergence corresponded with recognized geographic features that likely isolated populations, such as the Cordillera Central, the majority (74%) of lowland splits were between eastern and western populations. The timing of these events did not coincide across taxa, suggesting that historical events, such as the formation of the Isthmus of Panama and Pleistocene climatic cycles, were not the primary drivers of speciation. Rather, we observed that forest species, understory species, insectivores, and strongly territorial species- all traits associated with lower dispersal ability- were all more likely to have multiple BINs in Panama, suggesting strong ecological associations with divergences. Additionally, hand-wing index, a proxy for dispersal capability, was significantly lower in species with multiple BINs. These results suggest that dispersal ability plays an important role in generating diversity in Neotropical birds. Together, these results underscore the need for evolutionary studies of tropical bird communities to consider ecological factors along with geographic explanations, and that even in areas with well-known avifauna, avian diversity may be substantially underestimated.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds

McLaughlin

Aguilar

Bernstein

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Genetic studies have uncovered hidden biodiversity where morphological studies alone have failed to do so (e.g. López et al, 2015;Saitoh et al, 2015;Toews and Irwin, 2008), even within well-studied species complexes (e.g. Saetre et al, 2001;Salzburger et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

Phylogeography of the Vermilion Flycatcher species complex: Multiple speciation events, shifts in migratory behavior, and an apparent extinction of a Galápagos-endemic bird species

Carmi

Witt

Jaramillo³

et al. 2016

Molecular Phylogenetics and Evolution

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The Vermilion Flycatcher (Pyrocephalus rubinus) is a widespread species found in North and South America and the Galápagos. Its 12 recognized subspecies vary in degree of geographic isolation, phenotypic distinctness, and migratory status. Some authors suggest that Galápagos subspecies nanus and dubius constitute one or more separate species. Observational reports of distinct differences in song also suggest separate species status for the austral migrant subspecies rubinus. To evaluate geographical patterns of diversification and taxonomic limits within this species complex, we carried out a molecular phylogenetic analysis encompassing 10 subspecies and three outgroup taxa using mitochondrial (ND2, Cyt b) and nuclear loci (ODC introns 6 through 7, FGB intron 5). We used samples of preserved tissues from museum collections as well as toe pad samples from museum skins. Galápagos and continental clades were recovered as sister groups, with initial divergence at ∼1mya. Within the continental clade, North and South American populations were sister groups. Three geographically distinct clades were recovered within South America. We detected no genetic differences between two broadly intergrading North American subspecies, mexicanus and flammeus, suggesting they should not be recognized as separate taxa. Four western South American subspecies were also indistinguishable on the basis of loci that we sampled, but occur in a region with patchy habitat, and may represent recently isolated populations. The austral migrant subspecies, rubinus, comprised a monophyletic mitochondrial clade and had many unique nuclear DNA alleles. In combination with its distinct song, exclusive song recognition behavior, different phenology, and an isolated breeding range, our data suggests that this taxon represents a separate species from other continental populations. Mitochondrial and nuclear genetic data, morphology, and behavior suggest that Galápagos forms should be elevated to two full species corresponding to the two currently recognized subspecies, nanus and dubius. The population of dubius is presumed to be extinct, and thus would represent the first documented extinction of a Galápagos-endemic bird species. Two strongly supported mitochondrial clades divide Galápagos subspecies nanus in a geographic pattern that conflicts with previous hypotheses that were based on plumage color. Several populations of nanus have recently become extinct or are in serious decline. Urgent conservation measures should seek to preserve the deep mitochondrial DNA diversity within nanus, and further work should explore whether additional forms should be recognized within nanus. Ancestral states analysis based on our phylogeny revealed that the most recent common ancestor of extant Vermilion Flycatcher populations was migratory, and that migratory behavior was lost more often than gained within Pyrocephalus and close relatives, as has been shown to be the case within Tyrannidae as a whole.

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Extreme mitogenomic divergence between two syntopic specimens of Arremon aurantiirostris (Aves: Emberizidae) in central Panama suggests possible cryptic species

Cited by 2 publications

References 14 publications

Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds

Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds

Phylogeography of the Vermilion Flycatcher species complex: Multiple speciation events, shifts in migratory behavior, and an apparent extinction of a Galápagos-endemic bird species

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