Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria?

Abstract

Obtaining accurate phylogenies and effective species discrimination using a small standardized set of plastid genes is challenging in evolutionarily young lineages. Complete plastid genome sequencing offers an increasingly easy-to-access source of characters that helps address this. The usefulness of this approach, however, depends on the extent to which plastid haplotypes track morphological species boundaries. We have tested the power of complete plastid genomes to discriminate among multiple accessions of 11 of 13 New Caledonian Araucaria species, an evolutionarily young lineage where the standard DNA barcoding approach has so far failed and phylogenetic relationships have remained elusive. Additionally, 11 nuclear gene regions were Sanger sequenced for all accessions to ascertain the success of species discrimination using a moderate number of nuclear genes. Overall, fewer than half of the New Caledonian Araucaria species with multiple accessions were monophyletic in the plastid or nuclear trees. However, the plastid data retrieved a phylogeny with a higher resolution compared to any previously published tree of this clade and supported the monophyly of about twice as many species and nodes compared to the nuclear data set. Modest gains in discrimination thus are possible, but using complete plastid genomes or a small number of nuclear genes in DNA barcoding may not substantially raise species discriminatory power in many evolutionarily young lineages. The big challenge therefore remains to develop techniques that allow routine access to large numbers of nuclear markers scaleable to thousands of individuals from phylogenetically disparate sample sets.

Analysis of Complete Chloroplast Genome Sequences Improves Phylogenetic Resolution in Paris (Melanthiaceae)

“…Similar results have also been observed from the whole chloroplast genome analysis of Pinus species (Parks et al, 2009), Araucaria species (Ruhsam et al, 2015), and Acasia species (Williams et al, 2016). Nevertheless, relatively lower node support within Paris s.s. was observed (MLBS = 80%, PP = 0.98, Figure 3 ).…”

“…The molecular differences in complete cp genome between plant species can offer promising evolutionary information (Jansen et al, 2007; Parks et al, 2009). As a result, the cp genomes sequencing could greatly improve the phylogenetic resolution at low taxonomic levels (Parks et al, 2009; Ruhsam et al, 2015; Williams et al, 2016). Nevertheless, using the complete cp genome to reconstruct evolutionary relationship in those phylogenetically and taxonomically difficult genera has been rarely investigated (Ruhsam et al, 2015; Williams et al, 2016).…”

“…As complete cp genome sequences can offer valuable information for the reconstruction of complex evolutionary relationships in plants, they have been widely used for plant phylogenetic analyses and species identification in recent years (Jansen et al, 2007; Moore et al, 2007, 2010; Parks et al, 2009; Nock et al, 2011; Yang et al, 2013; Ruhsam et al, 2015). In the current study, we sequenced the complete cp genomes of eleven Paris taxa and compared these with the previously reported cp genome of P. verticillata (Do et al, 2014).…”

Phylogenomic and Comparative Analyses of Complete Plastomes of Croomia and Stemona (Stemonaceae)

“…Thus, it is necessary to develop more highly variable genetic markers for determining the phylogenetic relationships and divergence times for Croomia . Nowadays, many phylogenetic relationships that remained unresolved with few loci have been clarified by using whole cp genome sequences [19,20,21]. Thus, whole cp genome sequences are increasingly being used in phylogeny reconstruction and providing hypervariable genetic markers for population genetic studies, especially in a group of recently-diverged species [22,23].…”

The complete chloroplast genome sequence of the threatened trident maple Acer buergerianum (Aceraceae)

“…In recent decades human activities have seriously destroyed natural habitats, leading to the loss and quick decline of a large number of natural populations of wild trident maple in China. As plant chloroplast sequences can provide helpful information to reconstruct complex evolutionary relationships, they have been widely applied for species identification and phylogenetic analysis during the past years (Jansen et al 2007;Moore et al 2007;Parks et al 2009;Ruhsam et al 2015). The information of chloroplast genomes has been extensively applied in understanding plant genetic diversity and conservation genetics (Ye et al 2014;.…”