2020
DOI: 10.1093/sysbio/syaa040
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Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics

Abstract: Abstract The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most … Show more

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Cited by 20 publications
(15 citation statements)
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“…Unfortunately, full Bayesian inference is impossible for genomic datasets due to computational limitations (Harrington et al 2016; Li et al 2020). Common approaches include (1) penalized-likelihood methods such as (Sanderson 2003) and (Smith and O’Meara 2012) (see for example Hamilton et al 2019; Alda et al 2019; Opatova et al 2020; Burbrink et al 2020); (2) approximate-likelihood methods as implemented in PAML (see for example Harrington et al 2016; McGowen et al 2020; Li et al 2020), and (3) full-likelihood Bayesian divergence time analysis using a relaxed clock model, as implemented in (Drummond et al 2012) and (Höhna et al 2016), on a subset of the available data (see for example Harrington et al 2016; Ericson et al 2020; Bianconi et al 2020).…”
Section: Introductionmentioning
confidence: 99%
See 1 more Smart Citation
“…Unfortunately, full Bayesian inference is impossible for genomic datasets due to computational limitations (Harrington et al 2016; Li et al 2020). Common approaches include (1) penalized-likelihood methods such as (Sanderson 2003) and (Smith and O’Meara 2012) (see for example Hamilton et al 2019; Alda et al 2019; Opatova et al 2020; Burbrink et al 2020); (2) approximate-likelihood methods as implemented in PAML (see for example Harrington et al 2016; McGowen et al 2020; Li et al 2020), and (3) full-likelihood Bayesian divergence time analysis using a relaxed clock model, as implemented in (Drummond et al 2012) and (Höhna et al 2016), on a subset of the available data (see for example Harrington et al 2016; Ericson et al 2020; Bianconi et al 2020).…”
Section: Introductionmentioning
confidence: 99%
“…Specifically, we will focus on different approaches to sub-sample the full AHE dataset. Several approaches to subsample the full dataset have been proposed: (1) choose a random subset of the loci (Harrington et al 2016; Alda et al 2019; Ericson et al 2020), (2) choose the most complete loci (Harrington et al 2016), and (3) choose the loci with lowest GC variation (Romiguier et al 2013). Additionally to the second and third option, we selected loci with a high phylogenetic accuracy to recover the established genus Photinus .…”
Section: Introductionmentioning
confidence: 99%
“…To derive the age of speciation events leading to the New Guinean passerine species, we used the terminal branch lengths from the most recent well‐sampled species‐level phylogenies of larger relevant clades (e.g., Ericson et al, 2020; Jønsson et al, 2016; Marki, Jønsson, Irestedt, Nguyen, et al, 2017). In the relatively small number of instances where there was a lack of a suitable phylogeny for these purposes, we blasted the mitochondrial sequences on GenBank to identify the closest relative.…”
Section: Methodsmentioning
confidence: 99%
“…Herein we address genomic divergence and adaptation in Archbold's bowerbird Amblyornis papuensis, Ptilonorhynchidae (nomenclature follows [10]), supposedly one of the rarest birds in New Guinea [11]. It inhabits frostprone high mountains at elevations between 2300 and 3660 m, higher than most birds in New Guinea [12][13][14].…”
Section: Introductionmentioning
confidence: 99%