Phormium tenax (harakeke, New Zealand flax: Asphodelaceae) has long been considered indigenous to New Zealand (including the Chatham Islands) and Norfolk Island. However, the indigeneity of P. tenax on Norfolk Island, in particular, has been challenged by an alternative hypothesis that it was introduced by East Polynesians prior to European colonisation. We tested this alternative hypothesis using a dated phylogenetic tree. We also tested whether dated phylogenetic trees of Phormium could be reconciled with vicariance explanations of its distribution. We examined near-complete plastid genome sequences of P. tenax, P. cookianumand related plants. We then undertook Bayesian and likelihood estimation of the age of the divergence between Norfolk Island and New Zealand accessions using fossil calibration, and separately using biogeographic calibration assuming vicariance explanations of trans-oceanic distributions. DNA sequences of Norfolk Island plants were invariant and nested well within the wider diversity of P. tenax. Estimates of divergence times using fossil calibration did not exclude a common ancestor as recent as the second millennium CE. DNA sequences of Chatham Islands P. tenax were also nested within the diversity of P. tenax from New Zealand, but age estimates were older for their divergence from New Zealand plants (around 20,000–400,000 years). Biogeographic calibrations resulted in extremely ancient ages (tens of billions of years) of deeper nodes within the tree or several orders of magnitude variation in rates among lineages. Our results are consistent with translocation of harakeke by East Polynesian people, but our analyses cannot exclude a Late Quaternary natural dispersal event, which might result in similar genetic patterns. Biogeographic calibrations based on the break-up of Gondwana imply major departures from contemporary ideas of Earth’s history, or orders of magnitude rate variation among lineages.

Abstract Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing method that has been increasingly used for phylogenomic studies. Unfortunately, current widely used pipelines for analysis of target enrichment data do not have a vigorous procedure to remove paralogs in target enrichment data. In this study, we develop a pipeline we call Putative Paralogs Detection (PPD) to better address putative paralogs from enrichment data. The new pipeline is an add-on to the existing HybPiper pipeline, and the entire pipeline applies criteria in both sequence similarity and heterozygous sites at each locus in the identification of paralogs. Users may adjust the thresholds of sequence identity and heterozygous sites to identify and remove paralogs according to the level of phylogenetic divergence of their group of interest. The new pipeline also removes highly polymorphic sites attributed to errors in sequence assembly and gappy regions in the alignment. We demonstrated the value of the new pipeline using empirical data generated from Hyb-Seq and the Angiosperms353 kit for two woody genera Castanea (Fagaceae, Fagales) and Hamamelis (Hamamelidaceae, Saxifragales). Comparisons of data sets showed that the PPD identified many more putative paralogs than the popular method HybPiper. Comparisons of tree topologies and divergence times showed evident differences between data from HybPiper and data from our new PPD pipeline. We further evaluated the accuracy and error rates of PPD by BLAST mapping of putative paralogous and orthologous sequences to a reference genome sequence of Castanea mollissima. Compared to HybPiper alone, PPD identified substantially more paralogous gene sequences that mapped to multiple regions of the reference genome (31 genes for PPD compared with 4 genes for HybPiper alone). In conjunction with HybPiper, paralogous genes identified by both pipelines can be removed resulting in the construction of more robust orthologous gene data sets for phylogenomic and divergence time analyses. Our study demonstrates the value of Hyb-Seq with data derived from the Angiosperms353 probe set for elucidating species relationships within a genus, and argues for the importance of additional steps to filter paralogous genes and poorly aligned regions (e.g., as occur through assembly errors), such as our new PPD pipeline described in this study. [Angiosperms353; Castanea; divergence time; Hamamelis; Hyb-Seq, paralogs, phylogenomics.]

Target sequence capture has emerged as a powerful method to sequence hundreds or thousands of genomic regions in a cost- and time-efficient approach. In most cases, however, targeted regions lack full sequence information for certain samples, due to taxonomic, laboratory, or stochastic factors. Loci lacking molecular data for a large number of samples are commonly excluded from downstream analyses, even though they may still contain valuable information. On the other hand, including data-poor loci may bias phylogenetic analyses. Here we use a target sequence capture dataset of an ecologically and taxonomically diverse group of spiny sunflowers (Asteraceae, or Compositae: Barnadesioideae) to test how the inclusion or exclusion of such data-poor loci affects phylogenetic inference. We investigate the sensitivity of concatenation and coalescent approaches to missing data with matrices of varying taxonomic completeness by filtering loci with different proportions of missing samples prior to data analysis. We find that missing data affect both the topology and branch support of the resulting phylogenies. The matrix containing all loci yielded the overall highest node support values, independently of the amount of missing nucleotides. These results provide empirical support to earlier suggestions based on single genes and data simulations that taxa with high amounts of missing data should not be readily dismissed as they can provide essential information for phylogenomic reconstruction.

The human pathogen Haemophilus influenzae was the main cause of bacterial meningitis in children and a major cause of worldwide infant mortality before the introduction of a vaccine in the 1980s. Although the occurrence of serotype b (Hib), the most virulent type of H. influenzae, has since decreased, reports of infections with other serotypes and non-typeable strains are on the rise. While non-typeable strains have been studied in-depth, very little is known of the pathogen’s evolutionary history, and no genomes dating prior to 1940 were available.