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Although vast technological advances have been made and genetic software packages are growing in number, it is not a trivial task to analyse SNP data. We announce a new r package, dartr, enabling the analysis of single nucleotide polymorphism data for population genomic and phylogenomic applications. dartr provides user-friendly functions for data quality control and marker selection, and permits rigorous evaluations of conformation to Hardy-Weinberg equilibrium, gametic-phase disequilibrium and neutrality. The package reports standard descriptive statistics, permits exploration of patterns in the data through principal components analysis and conducts standard F-statistics, as well as basic phylogenetic analyses, population assignment, isolation by distance and exports data to a variety of commonly used downstream applications (e.g., newhybrids, faststructure and phylogeny applications) outside of the r environment. The package serves two main purposes: first, a user-friendly approach to lower the hurdle to analyse such data-therefore, the package comes with a detailed tutorial targeted to the r beginner to allow data analysis without requiring deep knowledge of r. Second, we use a single, well-established format-genlight from the adegenet package-as input for all our functions to avoid data reformatting. By strictly using the genlight format, we hope to facilitate this format as the de facto standard of future software developments and hence reduce the format jungle of genetic data sets. The dartr package is available via the r CRAN network and GitHub.

Aim To investigate biogeographic patterns of obligate freshwater fishes. Location Australia. Methods Similarity indices, parsimony analysis, and drainage‐based plots of species’ ranges were used to identify patterns. Results Relationships among regions were deduced largely by concordance between methodologies, then summarized into a proposed series of faunal provinces. Main conclusions The most striking pattern was in the incidence of endemism across the continent. Provinces in southern, central, and western Australia have high numbers of endemic fishes, presumably resulting from isolation by aridity and drainage divides. With exception of one region, northern and eastern Australia provinces have few endemics, probably explained in the north by high drainage connectivity during times of lowered sea levels. This does not account for low endemism in the east because drainages appear to have remained isolated during lowered sea levels and patterns suggest an absence of distinct barriers of other kinds. By default, climate again seems the most probable cause of species’ distributional limits. Whatever the case, most patterns were almost certainly established in the distant past, perhaps as early as Miocene. Influences of Plio–Pleistocene events on broad patterns of freshwater fish distributions seem minimal.

Theoretical efforts and small‐scale experiments have given rise to the widespread belief that the fewer occurrences a species has or the more fragmented its distribution is, the more vulnerable that species should be to extinction. Lacking, however, are large‐scale multi‐species studies exploring the connection between rarity and local extinction risk. Here we present a landscape‐level biogeographic test of this widely assumed linkage. Using a unique data set detailing the occurrence patterns of freshwater fishes of the Sonoran Desert (a gravely endangered fauna) we obtained for each of 25 species a measure of rarity that was independent of spatial scale. We found that fragmentation was consistently associated with elevated extinction risk, whereas the number of occurrences exerted a significant effect only if fragmentation had not already been accounted for. Specifically, desert fish species with the most fragmented historic distributions were nearly five times more likely to suffer local extirpations (since 1980) than were species with more continuous distributions. These findings underscore what a strong link exists between spatial distribution and vulnerability to extinction, clarifying that the link exists even at the landscape level and across an entire biogeographic fauna.

No abstract

Understanding the evolutionary history of diversifying lineages and the delineation of evolutionarily significant units and species remains major challenges for evolutionary biology. Low-cost representational sampling of the genome for single nucleotide polymorphisms shows great potential at the temporal scales that are typically the focus of species delimitation and phylogeography. We apply these markers to a case study of a freshwater turtle, Emydura macquarii, whose systematics has so far defied resolution, to bring to light a dynamic system of substantive allopatric lineages diverging on independent evolutionary trajectories, but held back in the process of speciation by low level and episodic exchange of alleles across drainage divides on various timescales. In the context of low-level episodic gene flow, speciation is often reticulate, rather than a bifurcating process. We argue that species delimitation needs to take into account the pattern of ancestry and descent of diverging lineages in allopatry together with the recent and contemporary processes of dispersal and gene flow that retard and obscure that divergence. Underpinned by a strong focus on lineage diagnosability, this combined approach provides a means for addressing the challenges of incompletely isolated populations with uncommon, but recurrent gene flow in studies of species delimitation, a situation likely to be frequently encountered. Taxonomic decisions in cases of allopatry often require subjective judgements.Our strategy, which adds an additional level of objectivity before that subjectivity is applied, reduces the risk of taxonomic inflation that can accompany lineage approaches to species delimitation. K E Y W O R D S ddRAD-seq, hybridization, introgression, landscape genomics, Murray-Darling Basin, species boundaries S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section at the end of the article. How to cite this article: Georges A, Gruber B, Pauly GB, et al. Genomewide SNP markers breathe new life into phylogeography and species delimitation for the problematic short-necked turtles (Chelidae: Emydura) of eastern Australia.

Aim To determine biogeographical patterns in five closely related species in the fish genus Hypseleotris, and to investigate the relative roles of drainage divide crossings and movement during lowered sea levels between drainage basins and biogeographical provinces based on the phylogeographical patterns within the group. The high degree of overlap in the distributions and ecology of these species makes them ideal candidates for comparative phylogeographical study.Location Eastern, central and south-eastern Australia.Methods A total of 179 Hypseleotris individuals were sequenced from 45 localities for the complete mitochondrial cytochrome b gene and the first 30 base pairs of the threonine transfer RNA for a total of 1170 bp. Phylogenetic relationships were hypothesized using parsimony and Bayesian analyses.

The smelt genus Retropinna nominally includes three small (<150 mm) freshwater fish species endemic to south-eastern Australia and New Zealand. For the two Australian species, the broad range of R. semoni (Weber) on the mainland suggests some vulnerability to isolation and genetic divergence, whereas the apparent confinement of R. tasmanica McCulloch to Tasmania is curious if, as suspected, it is anadromous. Analyses of Australian material using allozyme electrophoresis show five genetically distinct species with contiguous ranges and no evidence of genetic exchange. Three occur along the eastern seaboard (including three instances of sympatry), another in coastal and inland south-eastern Australia and Tasmania, and a fifth species in the Lake Eyre Basin. There is no indication of a simple ‘tasmanica’ v. ‘semoni’ dichotomy, but instead a complex pattern involving discrete clusters for the Upper Murray plus Darling rivers, Lower Murray, Glenelg River and Tasmanian regions, with coastal western Victorian samples having varying affinity to these groups. The overall pattern is one of deep divergences among species and strong genetic sub-structuring within and provides a strong argument for extended studies to prepare for appropriate conservation measures.