Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness

Leite, Rafael N.; Kimball, Rebecca T.; Braun, Edward L.; Derryberry, Elizabeth P.; Hosner, Peter A.; Derryberry, Graham E.; Anciães, Marina; McKay, Jessica; Aleixo, Alexandre; Ribas, Camila C.; Brumfield, Robb T.; Cracraft, Joel

doi:10.1016/j.ympev.2020.107013

Cited by 21 publications

(13 citation statements)

References 80 publications

(122 reference statements)

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“…Within the manakins, Ohlson et al (2013) placed Pseudopipra as sister to the genus Ceratopipra , which includes five well-recognized species that are extensively codistribtuted with Pseudopipra. The montane origin of Pseudopipra may be congruent with the observation that Pseudopipra is the sister group to Ceratopipra, which is also broadly distributed in the Neotropical lowlands from Central America to the Atlantic Forest and has a montane sister group ( C. cornuta ) (Leite et al, 2021; Ohlson et al, 2013; Prum, 1992). The breakpoints among these Ceratopipra species are highly concordant with the breakpoints among the genetic clusters within the Pseudopipra complex that we have presented here, implying that these closely related taxa have components of their phylogeographic history in common.…”

Section: Discussionsupporting

confidence: 74%

“…The two most recent phylogenetic hypotheses of manakins based on mitochondrial and nuclear DNA sequences both placed Pseudopipra as sister group to the five species of Ceratopipra (Leite et al, 2021; Ohlson et al, 2013). While the higher level phylogeny and taxonomy of manakins has received significant attention (also see Tello et al, 2009), work exploring intraspecific genetic variation within manakins has been restricted to relatively few species (e.g.…”

Section: Introductionmentioning

confidence: 99%

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Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes

Berv

Campagna

Feo

et al. 2019

Preprint

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AbstractThe 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 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. Most of the genetic breakpoints we identify among populations coincide with physical barriers to gene flow previously associated with avian areas of endemism. The phylogenetic relationships among these populations imply a novel pattern of Andean origination for this group, with subsequent diversification into the Amazonian lowlands. Our analysis of genomic admixture and gene flow establishes a complex history of introgression between some western Amazonian populations. These reticulate processes confound our application of standard concatenated and coalescent phylogenetic methods and raise the question of whether a lineage in the western Napo area of endemism should be considered a hybrid species. Lastly, analysis of variation in vocal and plumage phenotypes in the context of our phylogeny supports the hypothesis that Pseudopipra is a species-complex composed of at least 8, and perhaps up to 17 distinct species which have arisen in the last ∼2.5 Ma.

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Section: Discussionsupporting

confidence: 74%

Section: Introductionmentioning

confidence: 99%

Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes

Berv

Campagna

Feo

et al. 2019

Preprint

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“…However, previous studies mainly focused on the resulting species tree and not on single genes ( e . g ., Leite et al 2021). Overall, we could not identify a single summary statistics as a reliable predictor for phylogenetic accuracy (Figure 3).…”

Section: Discussionmentioning

confidence: 99%

A Time-calibrated Firefly (Coleoptera: Lampyridae) Phylogeny: Using Genomic Data for Divergence Time Estimation

Höhna

Lower

Duchen

et al. 2021

Preprint

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Fireflies (Coleoptera: Lampyridae) consist of over 2,000 described extant species. A well-resolved phylogeny of fireflies is important for the study of their bioluminescence, evolution, and conservation. We used a recently published anchored hybrid enrichment dataset (AHE; 436 loci for 88 Lampyridae species and 10 outgroup species) and state-of-the-art statistical methods (the fossilized birth-death-range process implemented in a Bayesian framework) to estimate a time-calibrated phylogeny of Lampyridae. Unfortunately, estimating calibrated phylogenies using AHE and the latest and most robust time-calibration strategies is not possible because of computational constraints. As a solution, we subset the full dataset and applied three different strategies: using the most complete loci, the most homogeneous loci, and the loci with the highest accuracy to infer the well established Photinus clade. The estimated topology using the three data subsets agreed on almost all major clades and only showed minor discordance with less supported nodes. The estimated divergence times overlapped for all nodes that are shared between the topologies. Thus, divergence time estimation is robust as long as the topology inference is robust and any well selected data subset suffices. Additionally, we observed an unexpected amount of gene tree discordance between the 436 AHE loci. Our assessment of model adequacy showed that standard phylogenetic substitution models are not adequate for any of the 436 AHE loci which is likely to bias phylogenetic inferences. We performed a simulation study to explore the impact of (a) incomplete lineage sorting, (b) uniformly distributed and systematic missing data, and (c) systematic bias in the position of highly variable and conserved sites. For our simulated data, we observed less gene tree variation and hence the empirically observed amount of gene tree discordance for the AHE dataset is unexpected.

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“…Selection tests were performed to identify evidence of positive selection related to either the evolution of nocturnality or visual adaptation specific to manakins, including high‐speed vision. A tree of all 46 of our ingroup taxa was constructed based on published phylogenies of relevant groups (Figure 2; Kimball et al, 2019; Leite et al, 2021; McKay et al, 2010; Ohlson et al, 2013; Reddy et al, 2017; Silva et al, 2018; White & Braun, 2019). For the nocturnal selection tests, all but one manakin species (the one with the best coverage) was removed to avoid overrepresentation of Pipridae (Figure 2a).…”

Section: Methodsmentioning

confidence: 99%

A novel exome probe set captures phototransduction genes across birds (Aves) enabling efficient analysis of vision evolution

White

Batz

Braun

et al. 2021

Molecular Ecology Resources

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A major goal in evolutionary biology is to understand the link between DNA sequences (genotype) and phenotypes across the tree of life. Modern genomics makes it possible to examine patterns of molecular evolution for suites of functionally related genes (e.g., Feng et al., 2020; Zhang et al., 2014), but expanding those efforts to cover the diversity of life remains challenging. Although it might be ideal to generate very high-quality genome assemblies (e.g., Rhie et al., 2021) for large numbers of taxa for such comparisons, the

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Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness

Cited by 21 publications

References 80 publications

Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes

Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes

A Time-calibrated Firefly (Coleoptera: Lampyridae) Phylogeny: Using Genomic Data for Divergence Time Estimation

A novel exome probe set captures phototransduction genes across birds (Aves) enabling efficient analysis of vision evolution

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