Molecular phylogenetic analyses reveal multiple long-distance dispersal events and extensive cryptic speciation in Nervilia (Orchidaceae), an isolated basal Epidendroid genus

The terrestrial orchid genus Nervilia is diagnosed by its hysteranthous pattern of emergence but is nested among leafless myco-heterotrophic lineages in the lower Epidendroideae. Comprising at least 80 species distributed across Africa, Asia, and Oceania, the genus remains poorly known and plagued by vague and overlapping species circumscriptions, especially within each of a series of taxonomically intractable species complexes. Prior small-scale, exploratory molecular phylogenetic analyses have revealed the existence of cryptic species, but little is otherwise understood of its origin, the scale and timing of its biogeographic spread, or the palaeoclimatic factors that have shaped its ecology and given rise to contemporary patterns of occurrence. Here, we sample widely throughout the generic range, including material of equivocal identity and probable undescribed status, as well as multiple accessions referable to several widespread ‘macrospecies’, enabling an evaluation of taxonomic b..., Phylogenetic analysis
Alignments were constructed using the MAFFT multiple alignment plugin in Geneious v11.1.4 (Kearse et al., 2012), with subsequent adjustment by eye. We excluded two poly-A regions comprising 41 and 61 positions in the trnL–F and matK genes, respectively (Supplementary File S1). An incongruence length difference (ILD) test (Farris et al., 1995) was performed in PAUP* v4.0b10 (Swofford, 2003) to assess whether the individual matK and trnL–F data sets, and the ITS and combined cpDNA data sets (Supplementary File S1), reflect similar potential phylogenies; 1,000 replicates, each with 1,000 random addition sequence replicates and tree bisection-reconnection (TBR) branch swapping, were performed in each test, and a P value of <0.05 was considered significant (Sullivan, 1996; Darlu & Lecointre, 2002). A “hard” incongruence test was also performed by directly comparing respective topologies, as well as resolution, for each clade generated in the separate analyses, wi..., , # Molecular phylogenetic analyses reveal multiple long-distance dispersal events and extensive cryptic speciation in *Nervilia (Orchidaceae), an isolated basal Epidendroid genus*

[https://doi.org/10.5061/dryad.tb2rbp0bn](https://doi.org/10.5061/dryad.tb2rbp0bn)

## Description of the files

Note that some of the files listed below are found in the Related Works section of this dataset.

### Files for phylogenetic alignment matrix

Alignments were constructed using the MAFFT multiple alignment plugin in Geneious v11.1.4 (Kearse et al., 2012), with subsequent adjustment by eye.

* Nervilia_trnLF90.fasta
* Nervilia_matK.fasta
* Nervilia_ITS81.fasta

### Files for phylogenetic tree results

Phylogenetic analysis of individual and multilocus alignments was carried out using MP in PAUP* v4.0b10 and BI in MrBayes v3.2 (Huelsenbeck & Ronquist, 2003). For MP analyses, heuristic searches were conducted with 1,000 random addition replicates followed by TBR branch swapping. All characters were...