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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A central question in conservation is how best to manage biodiversity, despite human domination of global processes (= Anthropocene). Common responses (i.e. translocations, genetic rescue) forestall potential extirpations, yet have an uncertain duration. A textbook example is the greater prairie chicken (GRPC: Tympanuchus cupido pinnatus), where translocations (1992–1998) seemingly rescued genetically depauperate Illinois populations. We re-evaluated this situation after two decades by genotyping 21 microsatellite loci from 1831 shed feathers across six leks in two counties over 4 years (2010–2013). Low migration rates (less than 1%) established each county as demographically independent, but with declining-population estimates (4 year average N = 79). Leks were genetically similar and significantly bottlenecked, with low effective population sizes (average Ne = 13.1; 4 year Ne/N = 0.166). Genetic structure was defined by 12 significantly different family groups, with relatedness r = 0.31 > half-sib r = 0.25. Average heterozygosity, indicating short-term survival, did not differ among contemporary, pre- and post-translocated populations, whereas allelic diversity did. Our results, the natural history of GRPC (i.e. few leks, male dominance hierarchies) and its controlled immigration suggest demographic expansion rather than genetic rescue. Legal protection under the endangered species act (ESA) may enhance recovery, but could exacerbate political–economic concerns on how best to manage ‘conservation-reliant’ species, for which GRPC is now an exemplar.

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Species are indisputable units for biodiversity conservation, yet their delimitation is fraught with both conceptual and methodological difficulties. A classic example is the taxonomic controversy surrounding the Gila robusta complex in the lower Colorado River of southwestern North America. Nominal species designations were originally defined according to weakly diagnostic morphological differences, but these conflicted with subsequent genetic analyses. Given this ambiguity, the complex was re-defined as a single polytypic unit, with the proposed ‘threatened’ status under the U.S. Endangered Species Act of two elements being withdrawn. Here we re-evaluated the status of the complex by utilizing dense spatial and genomic sampling (N = 387 and &gt;22k loci), coupled with SNP-based coalescent and polymorphism-aware phylogenetic models. In doing so, we found that all three species were indeed supported as evolutionarily independent lineages, despite widespread phylogenetic discordance. To juxtapose this discrepancy with previous studies, we first categorized those evolutionary mechanisms driving discordance, then tested (and subsequently rejected) prior hypotheses which argued phylogenetic discord in the complex was driven by the hybrid origin of Gila nigra. The inconsistent patterns of diversity we found within G. robusta were instead associated with rapid Plio-Pleistocene drainage evolution, with subsequent divergence within the ‘anomaly zone’ of tree space producing ambiguities that served to confound prior studies. Our results not only support resurrection of the three species as distinct entities, but also offer an empirical example of how phylogenetic discordance can be categorized within other recalcitrant taxa, particularly when variation is primarily partitioned at the species-level.

The American box turtles (Terrapene spp.) consist of four historically recognized species based primarily on morphological data (Minx 1996): Terrapene carolina (Linnaeus), T. ornata (Agassiz), T. nelsoni (Stejneger), and T. coahuila (Schmidt & Owens). Each of these species is polytypic except for T. coahuila. Recently, the Placyk lab re-assessed the classification of Terrapene using molecular phylogenetic data, and suggested elevating a clade consisting of T. carolina triunguis (Agassiz), T. c. mexicana (Gray), and T. c. yucatana (Boulenger) to a distinct species: Terrapene mexicana ssp. (Martin et al. 2013). Our dataset included all Terrapene species and almost all of the subspecies (except for T. nelsoni klauberi), as well as large sample sizes and a wide geographic sampling for both mitochondrial (mt) and nuclear (nuc) DNA. The mtDNA Cytochrome b (Cytb) gene and a nucDNA intron from the Glyceraldehyde-3-phosphate-dehydrogenase (GAPD) gene were used for phylogenetic analyses, and indicated that the T. mexicana clade was highly divergent from the remainder of the original T. carolina clade. In addition, the Cytochrome c oxidase subunit 1 (COI) gene, which is used in many animals for DNA barcoding, was sequenced and used to calculate pairwise percent DNA sequence divergence between taxa. The barcoding data also strongly supported our suggested classification revisions. However, because possible introgression was detected for some of the individuals, T. mexicana was not recognized as a distinct species in a recent assessment of Testudines taxonomic updates (Fritz & Havaš 2013). The purpose of this treatise is to suggest that the possible presence of introgression seen in Martin et al. (2013) does not warrant disregarding T. mexicana as a unique species.