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BackgroundUnderstanding how species diversify is a long-standing question in biology. The allopatric speciation model is a classic hypothesis to explain the speciation process. This model supposes that there is no gene flow during the divergence process of geographically isolated populations. On the contrary, the speciation with gene flow model supposes that gene flow does occur during the speciation process. Whether allopatric species have gene flow during the speciation process is still an open question.MethodsWe used the genetic information from 31 loci of 24 Chinese Bamboo Partridges (Bambusicola thoracicus) and 23 Taiwan Bamboo Partridges (B. sonorivox) to infer the gene flow model of the two species, using the approximate Bayesian computation (ABC) model. The ecological niche model was used to infer the paleo-distribution during the glacial period. We also tested whether the two species had a conserved ecological niche by means of a background similarity test.ResultsThe genetic data suggested that the post-divergence gene flow between the two species was terminated before the mid-Pleistocene. Furthermore, our ecological niche modeling suggested that their ecological niches were highly conserved, and that they shared an overlapping potential distribution range in the last glacial maximum.ConclusionsThe allopatric speciation model cannot explain the speciation process of the two Bamboo Partridges. The results of this study supported a scenario in which speciation with gene flow occurring between the allopatric species and have contributed to our understanding of the speciation process.

Additional file 1: Table S1. Sample information. Table S2. Primer information. Table S3. Summary of nuclear genes. Table S4. Prior distributions of demographic parameters for all demographic models. Table S5. Command line for each model in the running msABC. Table S6. Records of original occurrencefor the two species. Table S7. Occurrence points used to construct theecological niche models. Table S8. Correlation coefficient of each environmental layer. Table S9. Morphological characteristics of the specimens.

Additional file 2: Figure S1. Study area and occurrences used for constructing the ecological niche of B. thoracicus in the current time. Figure S2. Study area and occurrences used for constructing the ecological niche of B. sonorivox in the current time. Figure S3. Study area and occurrences for constructing the ecological niche of both B. thoracicus and B. sonorivox in the LGM. Figure S4. Potential distribution area of B. thoracicus in the current time. Figure S5. Potential distribution area of B. sonorivox in the current time.