A phylogenomic analysis of Nepenthes (Nepenthaceae)

Abstract

Nepenthaceae is one of the largest carnivorous plant families and features ecological and morphological adaptations indicating an impressive adaptive radiation. However, investigation of evolutionary and taxonomic questions is hindered by poor phylogenetic understanding, with previous molecular studies based on limited loci and taxa. We use high-throughput sequencing with a target-capture methodology based on a 353-loci, probe set to recover sequences for 197 samples, representing 151 described or putative Nepenthes species. Phylogenetic analyses were performed using supermatrix and maximum quartet species tree approaches. Our analyses confirm five Western outlier taxa, followed by N. danseri, as successively sister to the remainder of the group.We also find mostly consistent recovery of two major Southeast Asian clades. The first contains common or widespread lowland species plus a Wallacean-New Guinean clade. Within the second clade, sects. Insignes and Tentaculatae are well supported, while geographically defined clades representing Sumatra, Indochina, Peninsular Malaysia, Palawan, Mindanao and Borneo are also consistently recovered. However, we find considerable conflicting signal at the site and locus level, and often unstable backbone relationships. A handful of Bornean taxa are inconsistently placed and require further investigation. We make further suggestions for a modified infra-generic classification of genus Nepenthes.

Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics

“…To date, other than in Schefflera, the Angiosperms-353 enrichment panel (Johnson et al, 2018) has only been tested at the species level in sedges (Cyperus; Larridon et al, 2020) and Old World pitcher plants (Nepenthes; Murphy et al, 2020) and at the population level (SNPs) in rice (Oryza; Van Andel et al, 2019). When comparing data matrices containing on-target loci only, both Larridon et al (2020) and Murphy et al (2020) had a higher capture success (Table 3); an expected result since they worked with a greater proportion of silica-dried tissue (Brewer et al, 2019).…”

“…To overcome this design and optimization hurdle, the Angiosperms-353 probe set was developed from available transcriptome and genome data (One Thousand Plant Transcriptomes Initiative, 2019)including twelve Apiales representatives, three of them (Hedera, Hydrocotyle, and Polyscias) in Araliaceae -with universal probes that capture 353 nuclear single-copy loci shared across all angiosperms (Johnson et al, 2018). By using the Angiosperms-353 sequence capture probes, our study is among the first to test the efficacy of this probe set to resolve species-level relationships from either historical herbarium specimens (Brewer et al, 2019;Larridon et al, 2020;Murphy et al, 2020) or fresh tissue (Van Andel et al, 2019).…”

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

“…In contrast to lineage‐specific probe sets, a universal angiosperm‐wide set for anchored hybrid enrichment of ~400 loci has been developed (Buddenhagen et al., ) that has been successfully applied to a number of studies, for example for Aristolochia L. (Wanke et al., ) and Protea L. (Mitchell et al., ). More recently, a universal kit for Hyb‐Seq has also become available that is parsimony informative at the infrageneric level across potentially all angiosperm families, including Linaceae, Onagraceae, Portulacaceae, and Poaceae (Johnson et al., ), as well as Nepenthes L. (Murphy et al., ). Studies on Erica L. (Kadlec et al., ) and Buddlejeae (Chau et al., ) suggest that a lineage‐specific probe design strategy provides more markers that are phylogenetically informative at lower taxonomic levels, compared to universal probe sets.…”

Nepenthes maximoides(Nepenthaceae) a new, Critically Endangered (Possibly Extinct) species in Sect.Alataefrom Luzon, Philippines showing striking pitcher convergence withN. maxima(Sect.Regiae) of Indonesia

“…Information on the likely location of the collection was gathered by analysing other herbarium specimens collected by H.M. Curran recorded on JStor Global Plants (2020) Differing from Nepenthes graciliflora Elmer in the upper pitchers infundibulate-cylindrical, widest in the distal half at the peristome (not ovoid-cylindric, widest in the proximal half), the peristome broad, flattened, and lobed on the outer edge (not narrowly cylindrical and entire on the outer edge), the lid with a hooked basal appendage and a filiform apical appendage (not symmetrical, and absent, respectively). -Type: Curran s.n., Herb.…”

“…Mount Banahaw lies on the boundary between Tayabas (now Quezon) and Laguna Provinces. Of the 42 H.M. Curran specimens recorded from Laguna Province on JStor Global Plants (2020), 12 are also from Mt Banahaw. Therefore, on the basis of the JStor data, Mt Banahaw is the only collection location in former Tayabas Province that was a Curran location where Nepenthes might have been expected to be found (above 1000 m alt.).…”