Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of <i>Artocarpus</i>

Kates, Heather R.; Johnson, Matthew G.; Gardner, Elliot M.; Zerega, Nyree J. C.; Wickett, Norman J.

doi:10.1002/ajb2.1068

Cited by 70 publications

(69 citation statements)

References 49 publications

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“…Furthermore, Kates et al. () provide a framework to infer phased alleles from target enrichment data to investigate allelic diversity in a Hyb‐Seq data set.…”

Section: Discussionmentioning

confidence: 99%

An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

et al. 2019

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2019. An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae. Applications in Plant Sciences 7(10): e11295. PREMISE:Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here. METHODS:Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae. RESULTS:Alignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. DISCUSSION:The approach used to build a Hyb-Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage-specific.

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“…Furthermore, Kates et al. () provide a framework to infer phased alleles from target enrichment data to investigate allelic diversity in a Hyb‐Seq data set.…”

Section: Discussionmentioning

confidence: 99%

An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

et al. 2019

View full text Add to dashboard Cite

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“…Coding sequences were predicted with Augustus (Stanke et al, 2004), using Arabidopsis thaliana genes as a reference. A seven-way orthology search was carried out with ProteinOrtho5 (Lechner et al, 2011) using all CDS over 200 bp from the de novo assemblies in addition to the Artocarpus HybPiper (Johnson et al, 2016) reference from Kates et al (Kates et al, 2018). Orthologs present in at least three taxa were included in a new seven-taxon HybPiper reference consisting of in-frame CDS.…”

Section: Methodsmentioning

confidence: 99%

Long-distance dispersal shaped the diversity of tribe Dorstenieae (Moraceae)

Zhang

Gardner

Zerega

et al. 2019

Preprint

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1 Aim: The Neotropics have the highest terrestrial biodiversity on earth. Investigating the 2 relationships between the floras of the Neotropics and other tropical areas is critical to 3 understanding the origin and evolution of this mega-diverse region. Tribe Dorstenieae (Moraceae) 4 has a pantropical distribution and almost equal number of species on both sides of the Atlantic.5In this study, we investigate the relationship between the African and Neotropical floras using 6 Dorstenieae (15 genera, 156 species, Moraceae) as a model clade. 7 Location: the Neotropics and Africa. 8 Methods: We used a targeted enrichment strategy with herbarium samples and a nuclear bait set 9 to assemble a data set of 102 genes sampled from 83 (53%) species and fifteen genera (100%) of 10 Dorstenieae, and five outgroup species. Phylogenetic relationships were reconstructed with 11 maximum likelihood and coalescent approaches. This phylogeny was dated with a Bayesian 12 relaxed clock model and four fossil calibrations. The biogeographic history of the group was 13 then reconstructed with several dispersal-extinction-cladogenesis models (incl. DEC and DEC+J).14 Results: The crown-group ages of Dorstenieae and Dorstenia were estimated in the Cretaceous 15 (65.8-79.8 Ma) and the Paleocene (50.8-67.3 Ma), respectively. Tribe Dorstenieae as a whole 16 appears to have originated in the joint area of continental Africa, Madagascar and Asia-Oceania 17 area. The Neotropical species of Dorstenia diversified in the Eocene (29.8-44.7 Ma) and formed a 18 clade nested within the African lineages in the genus. Brosimum s.l., with a crown-group age at 19 the period of the Oligocene and Miocene (14.9-31.1 Ma), represents another Neotropical clade in 20 Dorstenieae. Main conclusions: Tribe Dorstenieae originated in the joint area of continental Africa, 1 Madagascar and Asia-Oceania area in the Cretaceous and then dispersed into Neotropics twice. 2 Neotropical diversification after long-distance dispersal across the Atlantic is the most plausible 3 explanation for the extant distribution pattern of Dorstenieae.4 5

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“…However, standard practice in microbial variant calling pipelines is to report only homozygous variants for downstream analysis, with heterozygous SNPs typically ignored. Additionally, most phylogenetic reconstruction software treat heterozygous SNPs as missing or non-informative characters, even when encoded with IUPAC-ambiguous characters [50]. Our results provide unequivocal evidence that caution is needed in phylogenomic interpretation when dealing with potential strain mixtures.…”

Section: Resultsmentioning

confidence: 68%

Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality

Aziz

Currie

Mayo

et al. 2019

Preprint

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21Human-to-human transmission of the melioidosis bacterium, Burkholderia pseudomallei, is exceedingly 22 rare, with only a handful of suspected cases documented to date. Here, we used whole-genome sequencing 23 (WGS) to characterise one such unusual B. pseudomallei transmission event, which occurred between a 24 breastfeeding mother with mastitis and her child. Two strains corresponding to multilocus sequence types 25 (STs) 259 and 261 were identified in the mother's sputum from both the primary culture sweep and in 26 purified colonies, confirming an unusual polyclonal infection in this patient. In contrast, primary culture 27 sweeps of the mother's breast milk and the child's cerebrospinal fluid and blood samples contained only 28 ST-259, indicating monoclonal transmission to the child. Analysis of purified ST-259 isolates showed no 29 genetic variation between mother and baby isolates, providing the strongest possible evidence of B. 30 pseudomallei transmission, probably via breastfeeding. Next, phylogenomic analysis of all isolates, 31 including the mother's mixed ST-259/261 sputum sample was performed to investigate the effects of 32 mixtures on phylogenetic inference. Inclusion of this mixture caused a dramatic reduction in the number 33 of informative SNPs, resulting in branch collapse of ST-259 and ST-261 isolates, and several instances of 34 incorrect topology in a global B. pseudomallei phylogeny, resulting in phylogenetic incongruence. Although 35 phylogenomics can provide clues about the presence of mixtures within WGS datasets, our results 36demonstrate that this methodology can lead to phylogenetic misinterpretation if mixed genomes are not 37 correctly identified and omitted. Using current bioinformatic tools, we demonstrate a robust method for 38 bacterial mixture identification and strain parsing that avoids these pitfalls. 393 Impact Statement 40Burkholderia pseudomallei is the causative agent of melioidosis, a tropical disease of high mortality. B. 41 pseudomallei infections occur almost exclusively through contact with contaminated soil and water. Using 42 whole-genome sequencing (WGS), we investigated a rare case of suspected B. pseudomallei transmission 43 from mother to child. The mother's sputum, breast milk and the baby's blood and cerebrospinal fluid (CSF) 44 specimens were collected, and DNA was extracted from both pure colonies and primary culture sweeps to 45 capture potential strain mixtures. In-depth analysis of genetic variants identified two strains in the mother's 46 sputum belonging to multilocus sequence types ST-259 and ST-261, whereas the child was infected with 47 only ST-259. Comparative genomics revealed no genetic differences between mother and child ST-259 48 isolates, providing the strongest possible evidence of transmission to the child via breast milk. The sputum 49 strain mixture was subsequently used to develop a bioinformatic method for identification and 50 quantification of mixtures from WGS data. Using this method, we found ST-259 and ST-261 at an 87%:13% 51 rat...

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Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus

Cited by 70 publications

References 49 publications

An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

Long-distance dispersal shaped the diversity of tribe Dorstenieae (Moraceae)

Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality

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