ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

Zhang, Chao; Rabiee, Maryam; Sayyari, Erfan; Mirarab, Siavash

doi:10.1186/s12859-018-2129-y

Cited by 1,782 publications

(1,695 citation statements)

References 48 publications

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“…To gauge the extent of ILS in our dataset, we performed concordance analyses using two different approaches. First, we used ASTRAL (Zhang, Rabiee, Sayyari, & Mirarab, ) to assess quartet support for the branch (i.e. the percentage of quartets in single‐locus trees which agree with the inferred concatenated tree).…”

Section: Resultsmentioning

confidence: 99%

New genome assembly of the barn owl (Tyto alba alba)

Ducrest

Neuenschwander

Schmid‐Siegert

et al. 2020

Ecology and Evolution

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New genomic tools open doors to study ecology, evolution, and population genomics of wild animals. For the Barn owl species complex, a cosmopolitan nocturnal raptor, a very fragmented draft genome was assembled for the American species (Tyto furcata pratincola) (Jarvis et al. 2014). To improve the genome, we assembled de novo Illumina and Pacific Biosciences (PacBio) long reads sequences of its European counterpart (Tyto alba alba). This genome assembly of 1.219 Gbp comprises 21,509 scaffolds and results in a N50 of 4,615,526 bp. BUSCO (Universal Single‐Copy Orthologs) analysis revealed an assembly completeness of 94.8% with only 1.8% of the genes missing out of 4,915 avian orthologs searched, a proportion similar to that found in the genomes of the zebra finch (Taeniopygia guttata) or the collared flycatcher (Ficedula albicollis). By mapping the reads of the female American barn owl to the male European barn owl reads, we detected several structural variants and identified 70 Mbp of the Z chromosome. The barn owl scaffolds were further mapped to the chromosomes of the zebra finch. In addition, the completeness of the European barn owl genome is demonstrated with 94 of 128 proteins missing in the chicken genome retrieved in the European barn owl transcripts. This improved genome will help future barn owl population genomic investigations.

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Section: Resultsmentioning

confidence: 99%

New genome assembly of the barn owl (Tyto alba alba)

Ducrest

Neuenschwander

Schmid‐Siegert

et al. 2020

Ecology and Evolution

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“…We generated 200 BS gene trees for each locus, with the termination condition parameter reduced by half the default value (i.e., genthreshfortopoterm = 10,000) (Zwickl, ). Gene trees were permitted to contain polytomies (collapsebranches = 1), which has been shown to improve species tree topology (Zhang et al, ). We inferred species trees from these optimal gene trees using the summary coalescent program ASTRAL‐III v5.6.1 (Mirarab et al, ; Sayyari & Mirarab, ; Zhang et al, ), with nodal support measured by the 200 multilocus BS replicates (Seo, ).…”

Section: Methodsmentioning

confidence: 99%

Phylogenomic analysis suggests Coreidae and Alydidae (Hemiptera: Heteroptera) are not monophyletic

2019

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Next‐generation sequencing technologies (NGS) allow systematists to amass a wealth of genomic data from non‐model species for phylogenetic resolution at various temporal scales. However, phylogenetic inference for many lineages dominated by non‐model species has not yet benefited from NGS, which can complement Sanger sequencing studies. One such lineage, whose phylogenetic relationships remain uncertain, is the diverse, agriculturally important and charismatic Coreoidea (Hemiptera: Heteroptera). Given the lack of consensus on higher‐level relationships and the importance of a robust phylogeny for evolutionary hypothesis testing, we use a large data set comprised of hundreds of ultraconserved element (UCE) loci to infer the phylogeny of Coreoidea (excluding Stenocephalidae and Hyocephalidae), with emphasis on the families Coreidae and Alydidae. We generated three data sets by including alignments that contained loci sampled for at least 50%, 60%, or 70% of the total taxa, and inferred phylogeny using maximum likelihood and summary coalescent methods. Twenty‐six external morphological features used in relatively comprehensive phylogenetic analyses of coreoids were also re‐evaluated within our molecular phylogenetic framework. We recovered 439–970 loci per species (16%–36% of loci targeted) and combined this with previously generated UCE data for 12 taxa. All data sets, regardless of analytical approach, yielded topologically similar and strongly supported trees, with the exception of outgroup relationships and the position of Hydarinae. We recovered a monophyletic Coreoidea, with Rhopalidae highly supported as the sister group to Alydidae + Coreidae. Neither Alydidae nor Coreidae were monophyletic; the coreid subfamilies Hydarinae and Pseudophloeinae were recovered as more closely related to Alydidae than to other coreid subfamilies. Coreinae were paraphyletic with respect to Meropachyinae. Most morphological traits were homoplastic with several clades defined by few, if any, synapomorphies. Our results demonstrate the utility of phylogenomic approaches in generating robust hypotheses for taxa with long‐standing phylogenetic problems and highlight that novel insights may come from such approaches.

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“…We analyzed the recovered genes using coalescent‐based and concatenated maximum likelihood (ML) methods; the latter is likely to result in misinferences if there are instances of incomplete lineage sorting (e.g., Maddison, ), but we included it as a point of reference for the coalescent analysis. We used ASTRAL‐III (Zhang et al., ) with default settings for coalescent‐based analyses on both the complete 264‐gene data set and on a partial 232‐gene data set that excluded genes with potential paralogs, and also for estimating branch support for the resulting species trees using both local posterior probabilities (LPP; Sayyari and Mirarab, ) and multi‐locus bootstrapping (MLB; Seo, ). LPPs measure support for a quadripartition (the four clusters around each internal branch in a species tree) and are computed using the proportion of gene‐tree quartets that agree or disagree with an internal branch.…”

Section: Methodsmentioning

confidence: 99%

A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

Gomez

Pokorny

Kantar³

et al. 2019

Appl Plant Sci

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Premise We developed a target enrichment panel for phylogenomic studies of Dioscorea , an economically important genus with incompletely resolved relationships. Methods Our bait panel comprises 260 low‐ to single‐copy nuclear genes targeted to work in Dioscorea , assessed here using a preliminary taxon sampling that includes both distantly and closely related taxa, including several yam crops and potential crop wild relatives. We applied coalescent‐based and maximum likelihood phylogenomic inference approaches to the pilot taxon set, incorporating new and published transcriptome data from additional species. Results The custom panel retrieved ~94% of targets and >80% of full gene length from 88% and 68% of samples, respectively. It has minimal gene overlap with existing panels designed for angiosperm‐wide studies and generally recovers longer and more variable targets. Pilot phylogenomic analyses consistently resolve most deep and recent relationships with strong support across analyses and point to revised relationships between the crop species D. alata and candidate crop wild relatives. Discussion Our customized panel reliably retrieves targeted loci from Dioscorea , is informative for resolving relationships in denser samplings, and is suitable for refining our understanding of the independent origins of cultivated yam species; the panel likely has broader promise for phylogenomic studies across Dioscoreales.

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ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

Cited by 1,782 publications

References 48 publications

New genome assembly of the barn owl (Tyto alba alba)

New genome assembly of the barn owl (Tyto alba alba)

Phylogenomic analysis suggests Coreidae and Alydidae (Hemiptera: Heteroptera) are not monophyletic

A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

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