Quantifying “demographic independence” is a vital step in establishing potential conservation units for a species in that it effectively distinguishes migration from within‐population reproduction. This is an important aspect because it allows for an accurate estimate of recruitment. For example, populations may be designated as 'management units' (=MUs) if indeed population growth results from local demography rather than immigration. Of additional interest is the calculation of immigrant ancestry and ascertainment of the temporal context over which immigration occurred. This is because MUs depend largely upon local (self‐sustaining) birth and death rates, and the quantification of ancestry is necessary to validate demographic independence. Dispersal rate is also of immediate interest to conservation biologists, and can be assessed by quantifying genetic divergence among populations. The capacity with which to gauge these benchmarks has now been extended herein to genome‐wide molecular data, in an attempt to adjust an analytical tool that was until now intractable for the next generation sequencing data. In this study, a popular legacy program for migrant detection (i.e. BayesAss3) has been modified to accept SNP (single nucleotide polymorphism) data. We validated BA3‐SNPs using empirical data to demonstrate its suitability for both high‐performance and desktop computing environments. We also facilitate high analytical throughput by presenting a binary search algorithm that automates MCMC (Markov chain Monte Carlo) parameter tuning. Our BA3‐SNPs‐autotune program required five or fewer rounds of optimization for 99% of input files, with acceptable mixing parameters derived in 100% of our test cases. Runtime for BA3‐SNPs is a function of the number of loci analysed. Benchmarking yielded an average runtime <32 hr (10 million MCMC generations) for datasets containing thousands of SNPs. The BA3 algorithm remains a viable option for analysing modern SNP datasets. Source code (C++ and Python) is released publicly under the GNU General Public License v3.0, and is available for download (Linux and Mac OSX) from the following URL: .

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BackgroundPorous species boundaries can be a source of conflicting hypotheses, particularly when coupled with variable data and/or methodological approaches. Their impacts can often be magnified when non-model organisms with complex histories of reticulation are investigated. One such example is the genus Catostomus (Osteichthys, Catostomidae), a freshwater fish clade with conflicting morphological and mitochondrial phylogenies. The former is hypothesized as reflecting the presence of admixed genotypes within morphologically distinct lineages, whereas the latter is interpreted as the presence of distinct morphologies that emerged multiple times through convergent evolution. We tested these hypotheses using multiple methods, to including multispecies coalescent and concatenated approaches. Patterson’s D-statistic was applied to resolve potential discord, examine introgression, and test the putative hybrid origin of two species. We also applied naïve binning to explore potential effects of concatenation.ResultsWe employed 14,007 loci generated from ddRAD sequencing of 184 individuals to derive the first highly supported nuclear phylogeny for Catostomus. Our phylogenomic analyses largely agreed with a morphological interpretation,with the exception of the placement of Xyrauchen texanus, which differs from both morphological and mitochondrial phylogenies. Additionally, our evaluation of the putative hybrid species C. columbianus revealed a lack introgression and instead matched the mitochondrial phylogeny. Furthermore, D-statistic tests clarified all discrepancies based solely on mitochondrial data, with agreement among topologies derived from concatenation and multispecies coalescent approaches. Extensive historic introgression was detected across six species-pairs. Potential endemism in the Virgin and Little Colorado Rivers was also apparent, and the former genus Pantosteus was derived as monophyletic, save for C. columbianus.ConclusionsComplex reticulated histories detected herein support the hypothesis that introgression was responsible for conflicts that occurred within the mitochondrial phylogeny, and explains discrepancies found between it and previous morphological phylogenies. Additionally, the hybrid origin of C. columbianus was refuted, but with the caveat that more fine-grain sampling is still needed. Our diverse phylogenomic approaches provided largely concordant results, with naïve binning useful in exploring the single conflict. Considerable diversity was found within Catostomus across southwestern North America, with two drainages [Virgin River (UT) and Little Colorado River (AZ)] reflecting unique composition.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1197-y) contains supplementary material, which is available to authorized users.

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