Phylogenomic history of enigmatic pygmy perches: implications for biogeography, taxonomy and conservation

Abstract

Pygmy perches (Percichthyidae) are a group of poorly dispersing freshwater fishes that have a puzzling biogeographic disjunction across southern Australia. Current understanding of pygmy perch phylogenetic relationships suggests past east–west migrations across a vast expanse of now arid habitat in central southern Australia, a region lacking contemporary rivers. Pygmy perches also represent a threatened group with confusing taxonomy and potentially cryptic species diversity. Here, we present the first study of the evolutionary history of pygmy perches based on genome-wide information. Data from 13 991 ddRAD loci and a concatenated sequence of 1 075 734 bp were generated for all currently described and potentially cryptic species. Phylogenetic relationships, biogeographic history and cryptic diversification were inferred using a framework that combines phylogenomics, species delimitation and estimation of divergence times. The genome-wide phylogeny clarified the biogeographic history of pygmy perches, demonstrating multiple east–west events of divergence within the group across the Australian continent. These results also resolved discordance between nuclear and mitochondrial data from a previous study. In addition, we propose three cryptic species within a southwestern species complex. The finding of potentially new species demonstrates that pygmy perches may be even more susceptible to ecological and demographic threats than previously thought. Our results have substantial implications for improving conservation legislation of pygmy perch lineages, especially in southwestern Western Australia.

The South American and Australian percichthyids and perciliids. What is new about them?

“…22) reveal that under the names Percilia gillissi and P. irwini are other cryptic species. Similar results have been published concerning Macquaria (Musyl, Keenan, 1992;Beheregaray et al, 2017), Gadopsis (Hammer et al, 2014;Unmack et al, 2017), and Nannoperca (Unmack et al, 2011;Buckley et al, 2018). Consequently, there is much more work needed to clarify the taxonomy of the South American and Australian percichthyids and perciliids.…”

“…Recent molecular studies suggested that there are cryptic species within Nannoperca (Unmack et al, 2011;. A phylogenomic study published recently confirmed the paraphyletic nature of N. vittata, revealing two new cryptic lineages within the species and recognizing informally the existence of N. 'flindersi' (Buckley et al, 2018). However, Buckley et al (2018) emphasized that a more comprehensive sampling may reveal the full geographic range of the delimited species, including morphological and ecological characters for establishing species boundaries.…”

“…These species are endemic to the southeast (e.g., Murray-Darling Basin and coastal drainages) and the southwest of Australia and have a puzzling biogeographic disjunction across southern Australia (Buckley et al, 2018;Fig. 9).…”

The lasting biological signature of Pliocene tectonics: Reviewing the re‐routing of Australia's largest river drainage system

“…because they have no close phylogenetic relatives; because they are relatively young lineages; and/or because they have sister lineages elsewhere in southern Victoria). These lineages include the phylogenetically highly divergent Ewens pygmy perch Nannoperca variegata (Buckley et al, ; Unmack, Hammer, Adams, & Dowling, ), an apparent relict species estimated to have diverged from its closest living relatives (including Murray‐Darling populations of Nannoperca australis ) some 15–20 mya (Buckley et al, ; although it is possible that a more recent sister lineage has gone extinct). Additional examples of SWV freshwater diversity include the western swamp crayfish ( Gramastacus insolitus ) which is restricted to southwestern Victoria and south‐eastern South Australia (Zeidler & Adams, ).…”

Brown trout phylogenetics: A persistent mirage towards (too) many species

“…Mitogenomes enable support to complex situations in which specific status was not previously assessed and/or ambiguous (e.g., Beheregaray et al, 2017;Buckley et al, 2018), and also provide support for a more integrative and corroborative taxonomy in which morphology and molecular species delineation have been shown to match (Pedraza-Marrón et al, 2019) or not (Vernygora et al, 2018).…”