Multiple origins of mountain biodiversity in New Zealand’s largest plant radiation

Aim: How mountains accumulate species diversity remains poorly understood, particularly the relative role of in situ cladogenesis compared with colonization from lower elevations. Here, we estimated the contributions of in situ cladogenesis and colonization in generating biodiversity of a large mountain plant radiation and determined the importance of niche adaptation and divergence in these processes. We expected cladogenesis would accompany novel habitats formed by mountain uplift but colonization would become more important with time as dispersal opportunities accrue.
Location: New Zealand, Southern Alps
Taxon: Veronica sect. Hebe (Plantaginaceae)
Methods: We estimated the most complete time-calibrated phylogeny to date for Veronica sect. Hebe to quantify rates of in situ cladogenesis and colonization of mountain habitat based on historical biogeographical models. We used environmental niche modeling to quantify species’ climate niches and estimate niche disparity and divergence over..., Phylogeny
We sampled 115 of 124 New Zealand species of Veronica by adding 38 newly sequenced species to the 77 in Thomas et al. (2021). We followed Thomas et al. (2021) for sample collection, DNA extraction, and sequencing. Briefly, we used target capture enrichment on recent herbarium and fresh collected samples using the Angiosperms353 bait kit that targets 353 low-copy nuclear genes (Johnson et al., 2018; McDonnell et al., 2021). Samples were sequenced on an Illumina NextSeq 500 with 2×150-bp paired-end reads. We processed sequences as in Thomas et al. (2021), retrieving target loci and flanking intron regions with HybPiper v1.2 (Johnson et al., 2016). We trimmed and filtered alignments using the “full” filtering scheme described in Thomas et al. (2021), which consisted of removing markers with taxon occupancy <50%, alignment length less than 150 bp and fewer than 20 parsimony informative sites, or average percent identity <65.5%.
To minimize gene tree conflict observed during ..., Alignments: text files; can be viewed with Geneious or Integrative Genomics Viewer
Tree files: text files; can be manipulated with R package ape or viewed with FigTree; posterior tree distribution can be visualized with DensiTree
Beauti XML: xml file; can be loaded with Beauti or run with BEAST2 software