Paralogs and Off-Target Sequences Improve Phylogenetic Resolution in a Densely Sampled Study of the Breadfruit Genus (Artocarpus, Moraceae)

Abstract

We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. Although codon partitioning did not result in any substantial topological differences, the inclusion of flanking noncoding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of data sets increased convergence between analysis methods but did not reduce gene-tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. Although the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of data sets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution. [Artocarpus; Moraceae; noncoding sequences; phylogenomics; target enrichment.]

New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq)

“…The corresponding full trees ( Figures 5 – 7 ; Supplementary Figures 1 – 5 ) show increased support for branches at deeper nodes and otherwise in particular an improved resolution and support for branches at shallow nodes, leading, in several cases, to a substantial improvement in the reconstruction of species relationships. This agrees with previous studies that highlighted the potential of supercontigs for improved statistical support ( Jones et al, 2019 ; Bagley et al, 2020 ; Gardner et al, 2021 ). Signal saturation at most of the deeper nodes and the opposing impact of discordant phylogenetic signals due to reticulate evolution at deeper and, in particular, at shallow nodes may explain the rather moderate impact of supercontigs on support values.…”

“…More importantly, in allopolyploids orthology, inference among duplicated loci (then being homoeologs, Glover et al, 2016 ) can be used to establish the origin of such lineages ( Yang and Smith, 2014 ; Morales-Briones et al, 2021 ). Depending on the design of the targets, the Hyb-Seq approach has the additional advantage of recovering not only targeted sets of loci that are highly conserved exons, but also parts of the more variable and flanking non-coding sequences (introns and intergenic spacers), hence, producing “supercontigs,” which can be aligned and analyzed together to amplify the phylogenetic signal ( Weitemier et al, 2014 ; Johnson et al, 2016 ; Jones et al, 2019 ; Bagley et al, 2020 ; Gardner et al, 2021 ). Moreover, this approach also allows the recovery of plastome data from off-target sequenced reads, enabling an independent estimate of phylogeny and inference from a principally and maternally inherited genome ( Weitemier et al, 2014 ; Mandel et al, 2015 ; Dillenberger et al, 2018 ; Herrando-Moraira et al, 2019 ).…”

Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica

“…Evolutionary network models are a promising alternative for resolving rapid radiations with hybridization, as they incorporate gene flow into the MSC model, but, again, remain limited by model complexity and high computational costs (Blair and Ané, 2020; Jiang et al, 2020). More complete taxon sampling may be a straightforward way to resolve incongruence in the presence of gene tree discordance (Hedtke et al, 2006; Gardner et al, 2020).…”

On the potential of Angiosperms353 for population genomic studies

“…Although it is possible to assess ploidy in target capture data using allele ratios (Viruel et al, 2019), our data did not have enough sequencing depth to use these methods. Ideally, paralogy of individual loci should also be investigated (Gardner et al, 2020), but this would require analysis with more than four individuals per species.…”