Pipridae (1 Viewer)

Sofia Marques Silva, Carlos Eduardo Agne, Alexandre Aleixo, Sandro L. Bonatto. Phylogeny and systematics of Chiroxiphia and Antilophia manakins (Aves, Pipridae)
Molecular Phylogenetics and Evolution. In Press, Accepted Manuscript, Available online 12 June 2018

Abstract

Chiroxiphia and Antilophia manakins are recognized as closely related genera. Nonetheless, Chiroxiphia has been recovered as paraphyletic in some studies with limited taxonomic coverage. This genus currently comprises five species, although this arrangement is still unsettled. Chiroxiphia pareola is the most widespread species, with four recognized subspecies, but their taxonomic status are also uncertain. Finally, the phylogenetic relationships amongst the majority of Chiroxiphia and Antilophia taxa are unknown. Here, we use multilocus DNA sequences from multiple individuals of all currently accepted species and subspecies of both genera to infer their phylogenetic relationships and its implications on their classification. Our results suggest Chiroxiphia, as currently defined, is a paraphyletic group, since C. boliviana is more closely related to Antilophia than to the remaining Chiroxiphia taxa. Within C. pareola, our results support that C. p. regina and C. p. napensis should be treated as independent species. We found three divergent clades in C. p. pareola likely corresponding to distinct subspecies: one in which the isolated and endemic Tobago Island C. p. atlantica individuals are grouped with C. p. pareola from the north bank of the lower Amazon River; and two sister clades comprising individuals distributed south of the Amazon river, and those from the Atlantic Forest.

Antilophia

Raposo do Amaral F., Maldonado-Coelho M., Aleixo A., Luna L.W., Sena do Rêgo P., Araripe J., Souza T.O., Silva W.A.G. & Thom G., in press. Recent chapters of Neotropical history overlooked in phylogeography: shallow divergence explains phenotype and genotype uncoupling in Antilophia manakins. Mol. Ecol.

There

Antilophia

Luna LW, Girão e Silva WA, Araripe J, Pereira ITF, d’Horta FM, Sampaio I, Schneider H, do Rêgo PS. 2018. Mutations in the melanocortin-1 receptor (MC1R) gene have no influence on the distinct patterns of melanic plumage found in the manakins of the genus Antilophia (Aves: Pipridae). An. Acad. Bras. Ciênc., 90: 2873-2879.
[full paper]

ABSTRACT
The melanocortin-1 receptor gene is the most widely-used marker for the investigation of the genetic determination of melanic plumage patterns. Studies of a number of wild bird species have shown an association between non-synonymous mutations of the MC1R gene and the presence of melanic variants. The genus Antilophia (Pipridae) includes only two manakin species (A. galeata and A. bokermanni), which are distinguished primarily by the differences in the pattern of melanic coloration of the plumage of the mantle in the adult males. In A. galeata, this plumage is black, while in A. bokermanni, it is predominantly white. This study investigates the possible association between mutations of the MC1R marker and the variation in plumage coloration observed in the two species. The MC1R sequences of the two species was analyzed, and the observed nucleotide variation was compared. Six polymorphic sites were identified, representing seven distinct genotypes. Five of these polymorphic mutations were non-synonymous, but were not related to the different phenotypes. Neutral evolution and the absence of any systematic association between the variants of the MC1R and plumage coloration in the Antilophia species indicate that alternative mechanisms regulate the expression of the coloration of the plumage in the adult males.
Key words: candidate gene, manakin, melanism, neutral evolution, plumage color.

Antilophia spp

Souza, T.O., Luna, L.W., Araripe, J. et al. Characterization of the genetic diversity and population structure of the manakin genus Antilophia through the development and analysis of microsatellite markers. J Ornithol (2019). https://doi.org/10.1007/s10336-019-01655-w

Abstract:

The two species of the genus Antilophia, Antilophia bokermanni and Antilophia galeata, are found in environments that are undergoing extensive modification, which may be provoking the loss of their genetic diversity. Nine polymorphic microsatellite loci were characterized and analyzed in each of these species. The distribution of allele frequencies revealed two clusters that reflected the distinct genetic profile of each species. Observed levels of heterozygosity were low for each species, with the lowest allelic diversity found in the critically endangered A. bokermanni. The set of loci described here, in contrast with other genetic markers that have been analyzed previously, effectively diagnosed the genetic diversity of different populations of the two species.

BirdLife's Globally Threatened Bird Forums

The newly described taxon Painted Manakin (Machaeropterus eckelberryi) is to be recognized as a species by BirdLife International.

Posted on May 23, 2019 by Red List Team (BirdLife International)

Painted Manakin (Machaeropterus eckelberryi) was discovered in 1996 in the Cordillera Azul of the Peruvian Andes. Based on its vocalisation and on genetic and morphological analysis, the species was described as a new taxon in 2017 (Lane et al. 2017).

Based on current information, Painted Manakin seems to be restricted to a small area in the foothills of the Andes in the departments of San Martín and Loreto in northern Peru, including the Cordillera Azul National Park (Lane et al. 2017). It is assumed that its range spans the ridges of the eastern flanks of the Cordillera Azul, Cordillera Escalera and the Mayo Valley at altitudes between c. 550 and 1,600 m (Lane et al. 2017). The population size has not been estimated.

Painted Manakin inhabits woodlands of up to 20 m canopy height on poor, sandy soils (Lane et al. 2017). It is frequently found near Melastomaceae trees, where it feeds on berries in the mid-story and canopy layer (Lane et al. 2017).

To date, there are no known threats to the species. Its preferred poor-soil woodland habitat is not suitable for agriculture and therefore not subject to the heavy logging that is currently ongoing, particularly in the Cordillera Azul (Lane et al. 2017, Moncrieff et al. 2018). Moreover, large parts of the range are protected in the Cordillera Azul National Park. Overall, Painted Manakin seems to be under much lower threat than other endemic species of the north-central Peruvian Andes, including the recently discovered Cordillera Azul Antbird (Myrmoderus eowilsoni) (Lane et al. 2017, Moncrieff et al. 2018).

Lepidothrix coronata

Camila Alves Reis, Cleyssian Dias, Juliana Araripe, Alexandre Aleixo, Marina Anciães, Iracilda Sampaio, Horacio Schneider, Péricles Sena do Rêgo. Multilocus data of a manakin species reveal cryptic diversification moulded by vicariance. Zoologica Scripta, First published: 15 November 2019|
https://doi.org/10.1111/zsc.12395

Abstract:

We used molecular tools and a multilocus approach to investigate the phylogeography of Lepidothrix coronata across most of its ample range. We sequenced six DNA fragments to produce phylogenies, molecular dating estimates, analyses of the dynamics of the demographic history of the species and a biogeographic analysis to estimate the events and changes in the ancestral distribution of the species. The results indicated the presence of four well‐established lineages, with high levels of divergence. These lineages are delineated by well‐defined geographic barriers, with one lineage, restricted to the west of the Andes, being the first to diverge from the complex. The other three lineages are exclusive to the Amazonian distribution of the species, with two being found north of the Amazon River, and the third, south of the Amazon. Some of the relationships found between these lineages were distinct from those described in previous studies. Important disagreements were found between the mtDNA phylogeny and that of the multilocus analysis, in relation to the lineages located to the west of the Andes. We propose that past introgression events may have influenced shifts in the relationships between lineages, despite the fact that the groups were well defined in both the phylogenies. The biogeographic analysis indicates that the lineages arose through successive vicariance events, which had a primary role in the diversification of the group. Two or three genetically structured subclades were also found within each Amazonian lineage, although these subclades are not isolated by an obvious geographic barrier.

Peter Kovalik said:

Camila Alves Reis, Cleyssian Dias, Juliana Araripe, Alexandre Aleixo, Marina Anciães, Iracilda Sampaio, Horacio Schneider, Péricles Sena do Rêgo. Multilocus data of a manakin species reveal cryptic diversification moulded by vicariance. Zoologica Scripta, First published: 15 November 2019|
https://doi.org/10.1111/zsc.12395

Abstract:

We used molecular tools and a multilocus approach to investigate the phylogeography of Lepidothrix coronata across most of its ample range. We sequenced six DNA fragments to produce phylogenies, molecular dating estimates, analyses of the dynamics of the demographic history of the species and a biogeographic analysis to estimate the events and changes in the ancestral distribution of the species. The results indicated the presence of four well‐established lineages, with high levels of divergence. These lineages are delineated by well‐defined geographic barriers, with one lineage, restricted to the west of the Andes, being the first to diverge from the complex. The other three lineages are exclusive to the Amazonian distribution of the species, with two being found north of the Amazon River, and the third, south of the Amazon. Some of the relationships found between these lineages were distinct from those described in previous studies. Important disagreements were found between the mtDNA phylogeny and that of the multilocus analysis, in relation to the lineages located to the west of the Andes. We propose that past introgression events may have influenced shifts in the relationships between lineages, despite the fact that the groups were well defined in both the phylogenies. The biogeographic analysis indicates that the lineages arose through successive vicariance events, which had a primary role in the diversification of the group. Two or three genetically structured subclades were also found within each Amazonian lineage, although these subclades are not isolated by an obvious geographic barrier.

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You know my email ^^

Pipra fasciicauda x Pipra aureola

Sampaio, L., Ferraz, D.O., da Costa, A.C.M. et al. Analyses of plumage coloration and genetic variation confirm the hybridization of Pipra fasciicauda and Pipra aureola in the Brazilian Amazon basin. J Ornithol (2020) doi:10.1007/s10336-020-01744-1

Abstract:

The present study aimed to confirm the occurrence of a hybridization event between the band-tailed manakin (Pipra fasciicauda) and the crimson-hooded manakin (Pipra aureola), based on the existence of a specimen that presents morphological traits of both taxa. We analyzed 297 taxidermized skins of adult males of the two species, including the potential hybrid. We also analyzed the mitochondrial (ND2, ND3 e COI) and nuclear (FGB-I5, MB-I2 e GAPDH-I3) genes of 12 adult specimens of the two taxa, diagnosed phenotypically, in addition to the potential hybrid. The analyses of the plumage indicated that the potential hybrid has an intermediate pattern of white banding on the tail that is less extensive than that found in Pipra fasciicauda, but that its other phenotypic traits are characteristic of Pipra aureola. The molecular topologies revealed two clades, one that groups P. aureola together with the potential hybrid, and the other that corresponds to P. fasciicauda. These findings allowed us to confirm the occurrence of a process of hybridization and potential introgression through secondary events in the P. aureola lineage.

Pseudopipra

Melanie said:

The mistaken manakin: a new genus-group name for Parus pipra Linnaeus, 1758 (Aves: Passeriformes: Pipridae)
GUY M. KIRWAN, NORMAND DAVID, STEVEN M. S. GREGORY, JAMES A. JOBLING, FRANK D. STEINHEIMER, GUILHERME RENZO ROCHA BRITO
Zootaxa Vol 4121, No 1 7 June 2016
http://dx.doi.org/10.11646/zootaxa.4121.1

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Proposal (848) to SACC

Change the genus of White-crowned Manakin from Dixiphia to Pseudopipra

Pseudopipra pipra

Jacob S. Berv, Leonardo Campagna, Teresa J. Feo, Ivandy Castro-Astor, Camila C. Ribas, Richard O. Prum, Irby J. Lovette. Genomic phylogeography of the White Crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes. bioRxiv, Posted July 24, 2019.
doi: https://doi.org/10.1101/713081

Abstract:

The complex landscape history of the Neotropics has generated opportunities for population isolation and subsequent diversification that place this region among the most species-rich in the world. Detailed phylogeographic studies are required to uncover the biogeographic histories of Neotropical taxa, to identify evolutionary correlates of diversity, and to reveal patterns of genetic connectivity, disjunction, and potential differentiation among lineages from different areas of endemism. The White-crowned Manakin (Pseudopipra pipra) is a small suboscine passerine bird that is broadly distributed through the subtropical rainforests of Central America, the lower montane cloud forests of the Andes from Colombia to central Peru, the lowlands of Amazonia and the Guianas, and the Atlantic forest of southeast Brazil. Pseudopipra is currently recognized as a single, polytypic biological species. We studied the effect of the historical and current Neotropical landscape on genetic and phenotypic differentiation within this species using genomic data derived from double digest restriction site associated DNA sequencing (ddRAD), and mitochondrial DNA. Our analyses identify five ancient clades, which encompass seventeen well-differentiated populations. Most of the breakpoints among populations coincide with physical barriers to gene flow previously associated with avian areas of endemism, and generally coincide with subspecies boundaries. The phylogenetic relationships among these populations imply a unique pattern of a montane Andean origin for the genus, with a subsequent expansion and radiation into the Amazonian lowlands. Analyses of genomic admixture demonstrate a complex history of introgression between some western Amazonian populations, which confound standard concatenated and coalescent phylogenetic analyses, and raise the possibility that a lineage in the western Napo area of endemism is of hybrid origin. Lastly, we analyze variation in vocal phenotypes in the context of our phylogeny and propose that Pseudopipra is a species-complex composed of 15-17 distinct species which have arisen in the last ∼2.5 Ma.

[pdf]

Yowser- need a detailed read through but bold proposal. Looks like they propose a minimum 8-way split!

Don't get too excited, Josh. This is the unreviewed manuscript (why on Earth would that be made public?!). It is fraught with many problems, not least of which was a very poor understanding of the taxonomy and biogeography of the complex, and was rejected by the journal. Haven't heard anything more about a re-submission anywhere.

Why wouldn't it be made public? Nothing too controversial about placing manuscripts on BioRxiv.

I don't know... If your manuscript is greatly flawed with simple issues, do you want the general public to see that? If it is rejected, or if the submission-to-publication time is particularly long with some journal, what is to stop some unscrupulous second party from simply lifting your idea or results and publishing them themselves? I can think of various reasons. It seems like waiting until the reviewed paper is accepted would be the time to release it publicly, if not *on the actual publication date*.

It's all a trade off. Sure, there may be issues with preprint manuscripts, that's totally normal. However there are many benefits. It allows for friendly review to improve the quality of the manuscript. They are given a DOI number and are citable, therefore preventing anyone 3rd parties from publishing the data under their own name. Finally, it is particularly useful for junior scientists such as masters students and PhD students who don't have the luxury of waiting months for the review process to add and demonstrate the presence of submission-ready manuscripts to CVs and for grant applications.

jacana said:

Why wouldn't it be made public? Nothing too controversial about placing manuscripts on BioRxiv.

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Preprints are pretty common in other fields of science (sometimes even the norm), so I don't see that being an issue. After all, its not like they published it on a geocities website or something...it's a legitimate archive.

Peter Kovalik said:

Proposal (848) to SACC

Change the genus of White-crowned Manakin from Dixiphia to Pseudopipra

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PASSED (14 May 2020)

Rafael N. Leite & al. (2020). Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness. Molecular Phylogenetics and Evolution. Available online 17 November 2020,
In Press, Journal Pre-proof.

https://www.sciencedirect.com/science/article/abs/pii/S1055790320302852

Abstract
Target capture sequencing effectively generates molecular marker arrays useful for molecular systematics. These extensive data sets are advantageous where previous studies using a few loci have failed to resolve relationships confidently. Moreover, target capture is well-suited to fragmented source DNA, allowing data collection from species that lack fresh tissues. Herein we use target capture to generate data for a phylogeny of the avian family Pipridae (manakins), a group that has been the subject of many behavioral and ecological studies. Most manakin species feature lek mating systems, where males exhibit complex behavioral displays including mechanical and vocal sounds, coordinated movements of multiple males, and high speed movements. We analyzed thousands of ultraconserved element (UCE) loci along with a smaller number of coding exons and their flanking regions from all but one species of Pipridae. We examined three different methods of phylogenetic estimation (concatenation and two multispecies coalescent methods). Phylogenetic inferences using UCE data yielded strongly supported estimates of phylogeny regardless of analytical method. Exon probes had limited capability to capture sequence data and resulted in phylogeny estimates with reduced support and modest topological differences relative to the UCE trees, although these conflicts had limited support. Two genera were paraphyletic among all analyses and data sets, with Antilophia nested within Chiroxiphia and Tyranneutes nested within Neopelma. The Chiroxiphia–Antilophia clade was an exception to the generally high support we observed; the topology of this clade differed among analyses, even those based on UCE data. To further explore relationships within this group, we employed two filtering strategies to remove low-information loci. Those analyses resulted in distinct topologies, suggesting that the relationships we identified within Chiroxiphia–Antilophia should be interpreted with caution. Despite the existence of a few continuing uncertainties, our analyses resulted in a robust phylogenetic hypothesis of the family Pipridae that provides a comparative framework for future ecomorphological and behavioral studies.

Hoping that the type species of Neopelma is sampled

Edit: no. Grumblllllllll ><

Chiroxiphia pareola

do Nascimento, N.F.F., Agne, C.E.Q., Batalha-Filho, H. et al. Population history of the Blue-backed Manakin (Chiroxiphia pareola) supports Plio-Pleistocene diversification in the Amazon and shows a recent connection with the Atlantic Forest. J Ornithol (2021). https://doi.org/10.1007/s10336-020-01845-x

Abstract:

It has been hypothesised that rivers serve as biogeographic barriers and Pleistocene forest refuges may explain the rich species diversity observed within Neotropical rainforests. The lack of correspondence between Amazonian and Atlantic forest species in South America is a good model for testing such hypotheses. We used molecular, ancestral area reconstruction, and potential paleodistribution analyses of Chiroxiphia pareola to test above hypotheses and examine the diversification and/or geographical expansion of populations. Six genes, two mitochondrial and four nuclear, were analysed. All population splits were estimated to have occurred in the Pliocene–Pleistocene period, and the occurrence of an Amazon population split was supported by historical river dynamics. Amazonian populations were not monophyletic, and the eastern Amazonian cluster was a sister of the Atlantic Forest population. Molecular divergence occurring between the Amazonian and Atlantic forest populations was low when compared to splits between the lineages separated by Amazonian rivers. During the early to middle Pleistocene era, regions associated with mountain slopes and riverbanks connected the Amazonian and Atlantic Forest populations near the interior of the Brazilian Northeast semiarid region, which might have facilitated species dispersal from Amazonia into the Atlantic Forest. After this point, the populations were separated, and the Atlantic Forest population remained stable until the end of the Pleistocene and Holocene eras when short-range expansion and demographic growth occurred. Our results provide evidence that highlights the role of rivers and historical climate change in the diversification of Amazonian and Atlantic Forest bird species through the Plio-Pleistocene era.

Peter Kovalik said:

Pseudopipra pipra

Jacob S. Berv, Leonardo Campagna, Teresa J. Feo, Ivandy Castro-Astor, Camila C. Ribas, Richard O. Prum, Irby J. Lovette. Genomic phylogeography of the White Crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes. bioRxiv, Posted July 24, 2019.
doi: Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes

Abstract:

The complex landscape history of the Neotropics has generated opportunities for population isolation and subsequent diversification that place this region among the most species-rich in the world. Detailed phylogeographic studies are required to uncover the biogeographic histories of Neotropical taxa, to identify evolutionary correlates of diversity, and to reveal patterns of genetic connectivity, disjunction, and potential differentiation among lineages from different areas of endemism. The White-crowned Manakin (Pseudopipra pipra) is a small suboscine passerine bird that is broadly distributed through the subtropical rainforests of Central America, the lower montane cloud forests of the Andes from Colombia to central Peru, the lowlands of Amazonia and the Guianas, and the Atlantic forest of southeast Brazil. Pseudopipra is currently recognized as a single, polytypic biological species. We studied the effect of the historical and current Neotropical landscape on genetic and phenotypic differentiation within this species using genomic data derived from double digest restriction site associated DNA sequencing (ddRAD), and mitochondrial DNA. Our analyses identify five ancient clades, which encompass seventeen well-differentiated populations. Most of the breakpoints among populations coincide with physical barriers to gene flow previously associated with avian areas of endemism, and generally coincide with subspecies boundaries. The phylogenetic relationships among these populations imply a unique pattern of a montane Andean origin for the genus, with a subsequent expansion and radiation into the Amazonian lowlands. Analyses of genomic admixture demonstrate a complex history of introgression between some western Amazonian populations, which confound standard concatenated and coalescent phylogenetic analyses, and raise the possibility that a lineage in the western Napo area of endemism is of hybrid origin. Lastly, we analyze variation in vocal phenotypes in the context of our phylogeny and propose that Pseudopipra is a species-complex composed of 15-17 distinct species which have arisen in the last ∼2.5 Ma.

[pdf]

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Berv, J.S., Campagna, L., Feo, T.J., Castro-Astor, I., Ribas, C.C., Prum, R.O., Lovette, I.J., Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes, Molecular Phylogenetics and Evolution (2021), doi: Redirecting