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.

Dramatic changes in climate, hydrology and topography have long been recognised to have lasting impacts on the diversity, distribution and divergence of species and populations (Pelletier et al., 2015).Understanding the relationship between the historical environment and the genealogy of species remains critical for interpreting how contemporary climate change may impact on species currently and in the near future. Most notably, increasing aridification and rising sea-levels (1-2 m increase by the end of the century; Overpeck & Weiss, 2009) predicted by climate change projections for many regions across the globe call into question the adaptive capacity and resilience of organisms, especially those with poor dispersal potential and narrow ranges (Davis et al., 2013;Falkenmark, 2013;Grummer et al., 2019). However, applying broadscale inferences about environmental changes to understand biodiversity resilience in the future is further complicated by spatial variation in environmental factors that might impact on how within-species responses

20While the influence of Pleistocene climatic changes on divergence and speciation 21 has been well-documented across the globe, complex spatial interactions between 22 hydrology and eustatics over longer timeframes may also determine species 23 evolutionary trajectories. Within the Australian continent, glacial cycles were not 24 associated with changes in ice cover and instead largely resulted in fluctuations from 25 moist to arid conditions across the landscape. Here, we investigate the role of 26 hydrological and coastal topographic changes brought about by Plio-Pleistocene 27 climatic changes on the biogeographic history of a small Australian freshwater fish, 28 the southern pygmy perch Nannoperca australis. Using 7,958 ddRAD-seq (double 29 digest restriction-site associated DNA) loci and 45,104 filtered SNPs, we combined 30 phylogenetic, coalescent and species distribution analyses to investigate the relative 31 roles of aridification, sea level and tectonics and their associated biogeographic 32 changes across southeast Australia. Sea-level changes since the Pliocene and 33 reduction or disappearance of large waterbodies throughout the Pleistocene were 34 determining factors in strong divergence across the clade, including the initial 35 formation and maintenance of a cryptic species, N. 'flindersi'. Isolated climatic 36 refugia and fragmentation due to lack of connected waterways maintained the 37 identity and divergence of inter-and intraspecific lineages. Our historical findings 38 suggest that predicted increases in aridification and sea level due to anthropogenic 39 climate change might result in markedly different demographic impacts, both 40 spatially and across different landscape types. 41 42

Background Understanding how species biology may facilitate resilience to climate change remains a critical factor in detecting and protecting species at risk of extinction. Many studies have focused on the role of particular ecological traits in driving species responses, but less so on demographic history and levels of standing genetic variation. Additionally, spatial variation in the interaction of demographic and adaptive factors may further complicate prediction of species responses to environmental change. We used environmental and genomic datasets to reconstruct the phylogeographic histories of two ecologically similar and largely co-distributed freshwater fishes, the southern (Nannoperca australis) and Yarra (N. obscura) pygmy perches, to assess the degree of concordance in their responses to Plio-Pleistocene climatic changes. We described contemporary genetic diversity, phylogenetic histories, demographic histories, and historical species distributions across both species, and statistically evaluated the degree of concordance in co-occurring populations. Results Marked differences in contemporary genetic diversity, historical distribution changes and historical migration were observed across the species, with a distinct lack of genetic diversity and historical range expansion suggested for N. obscura. Although several co-occurring populations within a shared climatic refugium demonstrated concordant demographic histories, idiosyncratic population size changes were found at the range edges of the more spatially restricted species. Discordant responses between species were associated with low standing genetic variation in peripheral populations. This might have hindered adaptive potential, as documented in recent demographic declines and population extinctions for the two species. Conclusion Our results highlight both the role of spatial scale in the degree of concordance in species responses to climate change, and the importance of standing genetic variation in facilitating range shifts. Even when ecological traits are similar between species, long-term genetic diversity and historical population demography may lead to discordant responses to ongoing and future climate change.

Aim: Anthropogenic climate change is forecast to drive regional climate disruption and instability across the globe. This issue is likely to be exacerbated within biodiversity hotspots, both due to the greater potential for species loss but also to the possibility that endemic lineages might not have experienced significant climatic variation in the past, limiting their evolutionary potential to respond to rapid climate change. We assessed the role of climatic stability on the accumulation and persistence of lineages in an obligate freshwater fish group endemic to a biodiversity hotspot. Location: Southwest Western Australia (SWWA). Taxa: Western pygmy perch (Nannoperca vittata) and little pygmy perch (Nannoperca pygmaea). Methods: We sampled 33 individuals from nine populations spanning the range of both study taxa to explore their phylogeographic history. Using a combination of genomic (ddRAD-seq) and environmental approaches, we investigated population divergence and phylogenetic relationships, delimited species and estimated changes in species distributions since the Pliocene. Results: We identified two deep phylogroups comprising three divergent clusters, which showed no historical connectivity since the Pliocene. We conservatively suggest these represent three isolated species with additional intraspecific structure within one widespread species. All lineages showed long-term patterns of isolation and persistence owing to climatic stability. Main conclusions: Our results highlighted the role of climatic stability in allowing the persistence of isolated lineages in the SWWA. This biodiversity hotspot is under compounding threat from ongoing climate change and habitat modification, which may further threaten previously undetected cryptic diversity across the region.