Abstract
BackgroundSpecies delimitation is a challenging but essential task in conservation biology. Morphologically similar species are sometimes difficult to recognize even after examination by experienced taxonomists. With the advent of molecular approaches in species delimitation, this hidden diversity has received much recent attention. In addition to DNA barcoding approaches, analytical tools based on the multi-species coalescence model (MSC) have been developed for species delimitation. Musa itinerans is widely distributed in subtropical Asia, and at least six varieties have been documented. However, the number of evolutionarily distinct lineages remains unknown.ResultsUsing genome resequencing data of five populations (making up four varieties), we examined genome-wide variation and found four varieties that were evolutionary significant units. A Bayesian Phylogenetics and Phylogeography (BP&P) analysis using 123 single copy nuclear genes support three speciation events of M. itinerans varieties with robust posterior speciation probabilities; However, a Bayes factor delimitation of species with genomic data (BFD*) analysis using 1201 unlinked single nucleotide polymorphisms gave decisive support for a five-lineage model. When reconciling divergence time estimates with a speciation time scale, a modified three-lineage model was consistent with that of BP&P, in which the speciation time of two varieties (M. itinerans var. itinerans and M. itinerans var. lechangensis) were dated to 26.2 kya and 10.7 kya, respectively. In contrast, other two varieties (M. itinerans var. chinensis and M. itinerans var. guangdongensis) diverged only 3.8 kya in the Anthropocene; this may be a consequence of genetic drift rather than a speciation event.ConclusionOur results showed that the M. itinerans species complex harbours high cryptic species diversity. We recommend that M. itinerans var. itinerans and M. itinerans var. lechangensis be elevated to subspecies status, and the extremely rare latter subspecies be given priority for conservation. We also recommend that the very recently diverged M. itinerans var. chinensis and M. itinerans var. guangdongensis should be merged under the subspecies M. itinerans var. chinensis. Finally, we speculate that species delimitation of recently diverged lineages may be more effective using genome-wide bi-allelic SNP markers with BFD* than by using unlinked loci and BP&P.
Highlights
Species delimitation is a challenging but essential task in conservation biology
Genome-wide polymorphisms among different morphological species Resequencing of 24 M. itinerans individuals from five populations generated a total of 2.75 billion filtered pair-end reads (249.7 Gb of filtered bases), and these short reads were mapped against the reference genome of M. itinerans with a mean unique mapping depth of 15.5, and coverage of 86.9%, (Additional file 1: Table S1)
When K = 2, samples of M. itinerans var. itinerans from the HN population were separated from the remaining continental populations (i.e. YC, LC: M. itinerans var. guangdongensis, ‘Musa itinerans var. guangdongensis (Mgd)’; CH: M. itinerans var. chinensis, ‘Musa itinerans var. chinensis (Mch)’; and BX: M. itinerans var. lechangensis, ‘Mlc’)
Summary
Species delimitation is a challenging but essential task in conservation biology. Morphologically similar species are sometimes difficult to recognize even after examination by experienced taxonomists. Accommodating the uncertainties in gene trees, the Bayesian Phylogenetics and Phylogeography program (BPP or BP&P) jointly estimates the posterior probability distributions of different species delimitation models and relevant parameters, including coalescent times and population sizes [10,11,12,13]. This program has been constantly updated and has been widely used in species delimitation studies of various taxonomic groups, including plants [14], birds [15], and insects [16]. A phylogeographic model test program that considers gene flow in a flexible model space has been developed (i.e. Phylogeographic Inference using Approximate Likelihoods, PHRAPL) [20, 21], the authors themselves have pointed out that PHRAPL may not be as powerful as BP&P in delimiting species with deep divergence times or weak migration rates
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